1
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Nam H, Lee E, Yang H, Lee K, Kwak T, Kim D, Kim H, Yang M, Yang Y, Son S, Nam YH, Minn I. PROMER technology: A new real-time PCR tool enabling multiplex detection of point mutation with high specificity and sensitivity. Biol Methods Protoc 2024; 9:bpae041. [PMID: 38938409 PMCID: PMC11208725 DOI: 10.1093/biomethods/bpae041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 05/21/2024] [Accepted: 06/02/2024] [Indexed: 06/29/2024] Open
Abstract
Real-time polymerase chain reaction (real-time PCR) is a powerful tool for the precise quantification of nucleic acids in various applications. In cancer management, the monitoring of circulating tumor DNA (ctDNA) from liquid biopsies can provide valuable information for precision care, including treatment selection and monitoring, prognosis, and early detection. However, the rare and heterogeneous nature of ctDNA has made its precise detection and quantification challenging, particularly for ctDNA containing hotspot mutations. We have developed a new real-time PCR tool, PROMER technology, which enables the precise and sensitive detection of ctDNA containing cancer-driven single-point mutations. The PROMER functions as both a PRObe and priMER, providing enhanced detection specificity. We validated PROMER technology using synthetic templates with known KRAS point mutations and demonstrated its sensitivity and linearity of quantification. Using genomic DNA from human cancer cells with mutant and wild-type KRAS, we confirmed that PROMER PCR can detect mutant DNA. Furthermore, we demonstrated the ability of PROMER technology to efficiently detect mutation-carrying ctDNA from the plasma of mice with human cancers. Our results suggest that PROMER technology represents a promising new tool for the precise detection and quantification of DNA containing point mutations in the presence of a large excess of wild-type counterpart.
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Affiliation(s)
- Hwanhee Nam
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD 21218, United States
| | - Esder Lee
- NuriBio Co., Ltd, Anyang-si, Gyeonggi-Do, 14058, Republic of Korea
| | - Hichang Yang
- NuriBio Co., Ltd, Anyang-si, Gyeonggi-Do, 14058, Republic of Korea
| | - Kyeyoon Lee
- NuriBio Co., Ltd, Anyang-si, Gyeonggi-Do, 14058, Republic of Korea
| | - Taeho Kwak
- NuriBio Co., Ltd, Anyang-si, Gyeonggi-Do, 14058, Republic of Korea
| | - Dain Kim
- NuriBio Co., Ltd, Anyang-si, Gyeonggi-Do, 14058, Republic of Korea
| | - Hyemin Kim
- NuriBio Co., Ltd, Anyang-si, Gyeonggi-Do, 14058, Republic of Korea
| | - Mihwa Yang
- NuriBio Co., Ltd, Anyang-si, Gyeonggi-Do, 14058, Republic of Korea
| | - Younjoo Yang
- NuriBio Co., Ltd, Anyang-si, Gyeonggi-Do, 14058, Republic of Korea
| | - Seungwan Son
- NuriBio Co., Ltd, Anyang-si, Gyeonggi-Do, 14058, Republic of Korea
| | - Young-Hyean Nam
- NuriBio Co., Ltd, Anyang-si, Gyeonggi-Do, 14058, Republic of Korea
| | - Il Minn
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD 21218, United States
- Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins Medical Institutions, Baltimore, MD 21287, United States
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2
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Ding X, Wang Y, Gui Y, Yang C. Two-Stage Mixed-Dye-Based Isothermal Amplification with Ribonuclease-Cleavable Enhanced Probes for Dual-Visualization Detection of SARS-CoV-2 Variants of Interest. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2401988. [PMID: 38829265 DOI: 10.1002/advs.202401988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Revised: 05/17/2024] [Indexed: 06/05/2024]
Abstract
Rapid and visual detection of SARS-CoV-2 variants is vital for timely assessment of variant transmission in resource-limited settings. Here, a closed-tube, two-stage, mixed-dye-based isothermal amplification method with ribonuclease-cleavable enhanced probes (REP), termed REP-TMAP, for dual-visualization detection of SARS-CoV-2 variants including JN.1, BA.2, BA.4/5, and Delta is introduced. The first stage of REP-TMAP is reverse transcription recombinase polymerase amplification and the second stage is dual-visualization detection synergistically mediated by the REP and the mixed dyes of cresol red and hydroxy naphthol blue. In REP-TMAP reaction, the color change under ambient light indicates SARS-CoV-2 infection, while the fluorescence change under blue light excitation specifies variant type. On detecting transcribed RNA of SARS-CoV-2 spike gene, this assay is rapid (within 40 min), highly sensitive (10-200 copies per reaction), and highly specific (identification of single-base mutations). Furthermore, the assay has been clinically validated to accurately detect JN.1, BA.2, and BA.4/5 variants from 102 human oropharyngeal swabs. The proposed assay therefore holds great potentials to provide a rapid, dual-visualization, sensitive, specific, point-of-care detection of SARS-CoV-2 variants and beyond.
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Affiliation(s)
- Xiong Ding
- Key Laboratory of Environmental Medicine and Engineering, Ministry of Education, Department of Nutrition and Food Hygiene, School of Public Health, Southeast University, Nanjing, 210009, P. R. China
| | - Yaru Wang
- Key Laboratory of Environmental Medicine and Engineering, Ministry of Education, Department of Nutrition and Food Hygiene, School of Public Health, Southeast University, Nanjing, 210009, P. R. China
| | - Yuxin Gui
- Key Laboratory of Environmental Medicine and Engineering, Ministry of Education, Department of Nutrition and Food Hygiene, School of Public Health, Southeast University, Nanjing, 210009, P. R. China
| | - Chuankun Yang
- Center of Clinical Laboratory Medicine, Zhongda Hospital, Southeast University, Nanjing, 210009, P. R. China
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3
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Rivero J, Cutillas C, Callejón R. New Insights on Tools for Detecting β-Tubulin Polymorphisms in Trichuris trichiura Using rhAmp TM SNP Genotyping. Animals (Basel) 2024; 14:1545. [PMID: 38891592 PMCID: PMC11171370 DOI: 10.3390/ani14111545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 05/20/2024] [Accepted: 05/20/2024] [Indexed: 06/21/2024] Open
Abstract
Soil-transmitted helminth (STH) infections, commonly treated with benzimidazoles, are linked to resistance through single nucleotide polymorphisms (SNPs) at position 167, 198, or 200 in the β-tubulin isotype 1 gene. The aim of this study was to establish a novel genotyping assay characterized by its rapidity and specificity. This assay was designed to detect the presence of SNPs within the partial β-tubulin gene of Trichuris trichiura. This was achieved through the biallelic discrimination at codons 167, 198, and 200 by employing the competitive binding of two allele-specific forward primers. The specificity and reliability of this assay were subsequently confirmed using Trichuris samples isolated from captive primates. Furthermore, a molecular study was conducted to substantiate the utility of the β-tubulin gene as a molecular marker. The assays showed high sensitivity and specificity when applied to field samples. Nevertheless, none of the SNPs within the β-tubulin gene were detected in any of the adult worms or eggs from the analyzed populations. All specimens consistently displayed an SS genotype. The examination of the β-tubulin gene further validated the established close relationships between the T. trichiura clade and Trichuris suis clade. This reaffirms its utility as a marker for phylogenetic analysis.
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Affiliation(s)
| | | | - Rocío Callejón
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Seville, 41012 Seville, Spain; (J.R.); (C.C.)
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4
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Pavel-Dinu M, Gardner CL, Nakauchi Y, Kawai T, Delmonte OM, Palterer B, Bosticardo M, Pala F, Viel S, Malech HL, Ghanim HY, Bode NM, Kurgan GL, Detweiler AM, Vakulskas CA, Neff NF, Sheikali A, Menezes ST, Chrobok J, Hernández González EM, Majeti R, Notarangelo LD, Porteus MH. Genetically corrected RAG2-SCID human hematopoietic stem cells restore V(D)J-recombinase and rescue lymphoid deficiency. Blood Adv 2024; 8:1820-1833. [PMID: 38096800 PMCID: PMC11006817 DOI: 10.1182/bloodadvances.2023011766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 10/23/2023] [Indexed: 04/10/2024] Open
Abstract
ABSTRACT Recombination-activating genes (RAG1 and RAG2) are critical for lymphoid cell development and function by initiating the variable (V), diversity (D), and joining (J) (V(D)J)-recombination process to generate polyclonal lymphocytes with broad antigen specificity. The clinical manifestations of defective RAG1/2 genes range from immune dysregulation to severe combined immunodeficiencies (SCIDs), causing life-threatening infections and death early in life without hematopoietic cell transplantation (HCT). Despite improvements, haploidentical HCT without myeloablative conditioning carries a high risk of graft failure and incomplete immune reconstitution. The RAG complex is only expressed during the G0-G1 phase of the cell cycle in the early stages of T- and B-cell development, underscoring that a direct gene correction might capture the precise temporal expression of the endogenous gene. Here, we report a feasibility study using the CRISPR/Cas9-based "universal gene-correction" approach for the RAG2 locus in human hematopoietic stem/progenitor cells (HSPCs) from healthy donors and RAG2-SCID patient. V(D)J-recombinase activity was restored after gene correction of RAG2-SCID-derived HSPCs, resulting in the development of T-cell receptor (TCR) αβ and γδ CD3+ cells and single-positive CD4+ and CD8+ lymphocytes. TCR repertoire analysis indicated a normal distribution of CDR3 length and preserved usage of the distal TRAV genes. We confirmed the in vivo rescue of B-cell development with normal immunoglobulin M surface expression and a significant decrease in CD56bright natural killer cells. Together, we provide specificity, toxicity, and efficacy data supporting the development of a gene-correction therapy to benefit RAG2-deficient patients.
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Affiliation(s)
- Mara Pavel-Dinu
- Division of Oncology, Hematology, Stem Cell Transplantation, Department of Pediatrics, Stanford University, Stanford, CA
| | - Cameron L. Gardner
- Immune Deficiency Genetics Section, Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Yusuke Nakauchi
- Division of Hematology, Department of Medicine, Cancer Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA
| | - Tomoki Kawai
- Immune Deficiency Genetics Section, Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Ottavia M. Delmonte
- Immune Deficiency Genetics Section, Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Boaz Palterer
- Immune Deficiency Genetics Section, Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Marita Bosticardo
- Immune Deficiency Genetics Section, Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Francesca Pala
- Immune Deficiency Genetics Section, Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Sebastien Viel
- Division of Oncology, Hematology, Stem Cell Transplantation, Department of Pediatrics, Stanford University, Stanford, CA
- Service d’immunologie biologique, Hospices Civils de Lyon, Centre International de Recherche en Infectivologie, Centre International de Recheerche in Infectivalogie, INSERM U1111, Université Claude Bernard Lyon 1, Centre National de la Recherge Scientifique, UMR5308, École Normale Supérieure de Lyon, University of Lyon, Lyon, France
| | - Harry L. Malech
- Genetic Immunotherapy Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Hana Y. Ghanim
- Division of Oncology, Hematology, Stem Cell Transplantation, Department of Pediatrics, Stanford University, Stanford, CA
| | | | | | | | | | | | - Adam Sheikali
- Division of Oncology, Hematology, Stem Cell Transplantation, Department of Pediatrics, Stanford University, Stanford, CA
| | - Sherah T. Menezes
- Division of Oncology, Hematology, Stem Cell Transplantation, Department of Pediatrics, Stanford University, Stanford, CA
| | - Jade Chrobok
- Division of Oncology, Hematology, Stem Cell Transplantation, Department of Pediatrics, Stanford University, Stanford, CA
| | - Elaine M. Hernández González
- Division of Oncology, Hematology, Stem Cell Transplantation, Department of Pediatrics, Stanford University, Stanford, CA
| | - Ravindra Majeti
- Division of Hematology, Department of Medicine, Cancer Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA
| | - Luigi D. Notarangelo
- Immune Deficiency Genetics Section, Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Matthew H. Porteus
- Division of Oncology, Hematology, Stem Cell Transplantation, Department of Pediatrics, Stanford University, Stanford, CA
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5
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Smekalova EM, Martinez MG, Combe E, Kumar A, Dejene S, Leboeuf D, Chen CY, Dorkin JR, Shuang LS, Kieft S, Young L, Barrera LA, Packer MS, Ciaramella G, Testoni B, Gregoire F, Zoulim F. Cytosine base editing inhibits hepatitis B virus replication and reduces HBsAg expression in vitro and in vivo. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102112. [PMID: 38292874 PMCID: PMC10825689 DOI: 10.1016/j.omtn.2023.102112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 12/21/2023] [Indexed: 02/01/2024]
Abstract
Chronic hepatitis B virus (HBV) infection remains a global health problem due to the lack of treatments that prevent viral rebound from HBV covalently closed circular (ccc)DNA. In addition, HBV DNA integrates in the human genome, serving as a source of hepatitis B surface antigen (HBsAg) expression, which impairs anti-HBV immune responses. Cytosine base editors (CBEs) enable precise conversion of a cytosine into a thymine within DNA. In this study, CBEs were used to introduce stop codons in HBV genes, HBs and Precore. Transfection with mRNA encoding a CBE and a combination of two guide RNAs led to robust cccDNA editing and sustained reduction of the viral markers in HBV-infected HepG2-NTCP cells and primary human hepatocytes. Furthermore, base editing efficiently reduced HBsAg expression from HBV sequences integrated within the genome of the PLC/PRF/5 and HepG2.2.15 cell lines. Finally, in the HBV minicircle mouse model, using lipid nanoparticulate delivery, we demonstrated antiviral efficacy of the base editing approach with a >3log10 reduction in serum HBV DNA and >2log10 reduction in HBsAg, and 4/5 mice showing HBsAg loss. Combined, these data indicate that base editing can introduce mutations in both cccDNA and integrated HBV DNA, abrogating HBV replication and silencing viral protein expression.
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Affiliation(s)
| | - Maria G. Martinez
- INSERM U1052, Cancer Research Center of Lyon, CNRS UMR 5286, 69008 Lyon, France
- University of Lyon, UMR_S1052, UCBL, 69008 Lyon, France
- Hepatology Institute of Lyon, 69008 Lyon, France
| | - Emmanuel Combe
- INSERM U1052, Cancer Research Center of Lyon, CNRS UMR 5286, 69008 Lyon, France
- University of Lyon, UMR_S1052, UCBL, 69008 Lyon, France
- Hepatology Institute of Lyon, 69008 Lyon, France
| | - Anuj Kumar
- INSERM U1052, Cancer Research Center of Lyon, CNRS UMR 5286, 69008 Lyon, France
- University of Lyon, UMR_S1052, UCBL, 69008 Lyon, France
- Hepatology Institute of Lyon, 69008 Lyon, France
| | | | | | | | | | | | | | | | | | | | | | - Barbara Testoni
- INSERM U1052, Cancer Research Center of Lyon, CNRS UMR 5286, 69008 Lyon, France
- University of Lyon, UMR_S1052, UCBL, 69008 Lyon, France
- Hepatology Institute of Lyon, 69008 Lyon, France
| | | | - Fabien Zoulim
- INSERM U1052, Cancer Research Center of Lyon, CNRS UMR 5286, 69008 Lyon, France
- University of Lyon, UMR_S1052, UCBL, 69008 Lyon, France
- Hepatology Institute of Lyon, 69008 Lyon, France
- Hepatology Department, Hospices Civils de Lyon (HCL), 69004 Lyon, France
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6
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Allen AG, Khan SQ, Margulies CM, Viswanathan R, Lele S, Blaha L, Scott SN, Izzo KM, Gerew A, Pattali R, Cochran NR, Holland CS, Zhao AH, Sherman SE, Jaskolka MC, Wu M, Wilson AC, Sun X, Ciulla DM, Zhang D, Nelson JD, Zhang P, Mazzucato P, Huang Y, Giannoukos G, Marco E, Nehil M, Follit JA, Chang KH, Shearman MS, Wilson CJ, Zuris JA. A highly efficient transgene knock-in technology in clinically relevant cell types. Nat Biotechnol 2024; 42:458-469. [PMID: 37127662 DOI: 10.1038/s41587-023-01779-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 04/04/2023] [Indexed: 05/03/2023]
Abstract
Inefficient knock-in of transgene cargos limits the potential of cell-based medicines. In this study, we used a CRISPR nuclease that targets a site within an exon of an essential gene and designed a cargo template so that correct knock-in would retain essential gene function while also integrating the transgene(s) of interest. Cells with non-productive insertions and deletions would undergo negative selection. This technology, called SLEEK (SeLection by Essential-gene Exon Knock-in), achieved knock-in efficiencies of more than 90% in clinically relevant cell types without impacting long-term viability or expansion. SLEEK knock-in rates in T cells are more efficient than state-of-the-art TRAC knock-in with AAV6 and surpass more than 90% efficiency even with non-viral DNA cargos. As a clinical application, natural killer cells generated from induced pluripotent stem cells containing SLEEK knock-in of CD16 and mbIL-15 show substantially improved tumor killing and persistence in vivo.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Meng Wu
- Editas Medicine, Cambridge, MA, USA
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7
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Dramé-Maigné A, Espada R, McCallum G, Sieskind R, Gines G, Rondelez Y. In Vitro Enzyme Self-Selection Using Molecular Programs. ACS Synth Biol 2024; 13:474-484. [PMID: 38206581 DOI: 10.1021/acssynbio.3c00385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2024]
Abstract
Directed evolution provides a powerful route for in vitro enzyme engineering. State-of-the-art techniques functionally screen up to millions of enzyme variants using high throughput microfluidic sorters, whose operation remains technically challenging. Alternatively, in vitro self-selection methods, analogous to in vivo complementation strategies, open the way to even higher throughputs, but have been demonstrated only for a few specific activities. Here, we leverage synthetic molecular networks to generalize in vitro compartmentalized self-selection processes. We introduce a programmable circuit architecture that can link an arbitrary target enzymatic activity to the replication of its encoding gene. Microencapsulation of a bacterial expression library with this autonomous selection circuit results in the single-step and screening-free enrichment of genetic sequences coding for programmed enzymatic phenotypes. We demonstrate the potential of this approach for the nicking enzyme Nt.BstNBI (NBI). We applied autonomous selection conditions to enrich for thermostability or catalytic efficiency, manipulating up to 107 microcompartments and 5 × 105 variants at once. Full gene reads of the libraries using nanopore sequencing revealed detailed mutational activity landscapes, suggesting a key role of electrostatic interactions with DNA in the enzyme's turnover. The most beneficial mutations, identified after a single round of self-selection, provided variants with, respectively, 20 times and 3 °C increased activity and thermostability. Based on a modular molecular programming architecture, this approach does not require complex instrumentation and can be repurposed for other enzymes, including those that are not related to DNA chemistry.
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Affiliation(s)
- Adèle Dramé-Maigné
- Gulliver UMR CNRS 7083, ESPCI Paris, Université PSL, 75005 Paris, France
| | - Rocío Espada
- Gulliver UMR CNRS 7083, ESPCI Paris, Université PSL, 75005 Paris, France
| | - Giselle McCallum
- Gulliver UMR CNRS 7083, ESPCI Paris, Université PSL, 75005 Paris, France
| | - Rémi Sieskind
- Gulliver UMR CNRS 7083, ESPCI Paris, Université PSL, 75005 Paris, France
| | - Guillaume Gines
- Gulliver UMR CNRS 7083, ESPCI Paris, Université PSL, 75005 Paris, France
| | - Yannick Rondelez
- Gulliver UMR CNRS 7083, ESPCI Paris, Université PSL, 75005 Paris, France
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8
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Fauser F, Kadam BN, Arangundy-Franklin S, Davis JE, Vaidya V, Schmidt NJ, Lew G, Xia DF, Mureli R, Ng C, Zhou Y, Scarlott NA, Eshleman J, Bendaña YR, Shivak DA, Reik A, Li P, Davis GD, Miller JC. Compact zinc finger architecture utilizing toxin-derived cytidine deaminases for highly efficient base editing in human cells. Nat Commun 2024; 15:1181. [PMID: 38360922 PMCID: PMC10869815 DOI: 10.1038/s41467-024-45100-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 01/15/2024] [Indexed: 02/17/2024] Open
Abstract
Nucleobase editors represent an emerging technology that enables precise single-base edits to the genomes of eukaryotic cells. Most nucleobase editors use deaminase domains that act upon single-stranded DNA and require RNA-guided proteins such as Cas9 to unwind the DNA prior to editing. However, the most recent class of base editors utilizes a deaminase domain, DddAtox, that can act upon double-stranded DNA. Here, we target DddAtox fragments and a FokI-based nickase to the human CIITA gene by fusing these domains to arrays of engineered zinc fingers (ZFs). We also identify a broad variety of Toxin-Derived Deaminases (TDDs) orthologous to DddAtox that allow us to fine-tune properties such as targeting density and specificity. TDD-derived ZF base editors enable up to 73% base editing in T cells with good cell viability and favorable specificity.
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Affiliation(s)
| | | | | | | | | | | | - Garrett Lew
- Sangamo Therapeutics, Inc., Brisbane, CA, USA
| | - Danny F Xia
- Sangamo Therapeutics, Inc., Brisbane, CA, USA
| | | | - Colman Ng
- Sangamo Therapeutics, Inc., Brisbane, CA, USA
| | | | | | | | | | | | | | - Patrick Li
- Sangamo Therapeutics, Inc., Brisbane, CA, USA
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9
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Lopes R, Prasad MK. Beyond the promise: evaluating and mitigating off-target effects in CRISPR gene editing for safer therapeutics. Front Bioeng Biotechnol 2024; 11:1339189. [PMID: 38390600 PMCID: PMC10883050 DOI: 10.3389/fbioe.2023.1339189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 12/29/2023] [Indexed: 02/24/2024] Open
Abstract
Over the last decade, CRISPR has revolutionized drug development due to its potential to cure genetic diseases that currently do not have any treatment. CRISPR was adapted from bacteria for gene editing in human cells in 2012 and, remarkably, only 11 years later has seen it's very first approval as a medicine for the treatment of sickle cell disease and transfusion-dependent beta-thalassemia. However, the application of CRISPR systems is associated with unintended off-target and on-target alterations (including small indels, and structural variations such as translocations, inversions and large deletions), which are a source of risk for patients and a vital concern for the development of safe therapies. In recent years, a wide range of methods has been developed to detect unwanted effects of CRISPR-Cas nuclease activity. In this review, we summarize the different methods for off-target assessment, discuss their strengths and limitations, and highlight strategies to improve the safety of CRISPR systems. Finally, we discuss their relevance and application for the pre-clinical risk assessment of CRISPR therapeutics within the current regulatory context.
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Affiliation(s)
- Rui Lopes
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Centre Basel, F Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Megana K Prasad
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Centre Basel, F Hoffmann-La Roche Ltd., Basel, Switzerland
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10
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Penter L, Borji M, Nagler A, Lyu H, Lu WS, Cieri N, Maurer K, Oliveira G, Al'Khafaji AM, Garimella KV, Li S, Neuberg DS, Ritz J, Soiffer RJ, Garcia JS, Livak KJ, Wu CJ. Integrative genotyping of cancer and immune phenotypes by long-read sequencing. Nat Commun 2024; 15:32. [PMID: 38167262 PMCID: PMC10762175 DOI: 10.1038/s41467-023-44137-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Accepted: 12/01/2023] [Indexed: 01/05/2024] Open
Abstract
Single-cell transcriptomics has become the definitive method for classifying cell types and states, and can be augmented with genotype information to improve cell lineage identification. Due to constraints of short-read sequencing, current methods to detect natural genetic barcodes often require cumbersome primer panels and early commitment to targets. Here we devise a flexible long-read sequencing workflow and analysis pipeline, termed nanoranger, that starts from intermediate single-cell cDNA libraries to detect cell lineage-defining features, including single-nucleotide variants, fusion genes, isoforms, sequences of chimeric antigen and TCRs. Through systematic analysis of these classes of natural 'barcodes', we define the optimal targets for nanoranger, namely those loci close to the 5' end of highly expressed genes with transcript lengths shorter than 4 kB. As proof-of-concept, we apply nanoranger to longitudinal tracking of subclones of acute myeloid leukemia (AML) and describe the heterogeneous isoform landscape of thousands of marrow-infiltrating immune cells. We propose that enhanced cellular genotyping using nanoranger can improve the tracking of single-cell tumor and immune cell co-evolution.
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Grants
- P01 CA229092 NCI NIH HHS
- P50 CA101942 NCI NIH HHS
- UM1 CA186709 NCI NIH HHS
- U24 CA224316 NCI NIH HHS
- U24 CA224331 NCI NIH HHS
- U24 CA224285 NCI NIH HHS
- R50 CA251956 NCI NIH HHS
- U24 CA224309 NCI NIH HHS
- U24 CA224319 NCI NIH HHS
- K08 CA245209 NCI NIH HHS
- This work was supported by National Institutes of Health, National Cancer Institute grant P01CA229092 (CJW), UM1CA186709 (Principal Investigator: Geoffrey Shapiro), National Cancer Institute Cancer Therapy Evaluation Program, Bristol-Myers Squibb, and LLS Therapy Accelerator Program. L.P. was supported by a research fellowship from the German Research Foundation (DFG, PE 3127/1-1) and is a Scholar of the American Society of Hematology, participant in the BIH Charité Digital Clinician Scientist Program funded by the DFG, the Charité – Universitätsmedizin Berlin, and the Berlin Institute of Health at Charité (BIH) and is supported by the Max-Eder program of the German Cancer Aid. A.A. is supported by the Broad Institute IGNITE award. K.M. is suppored by the ASCO YIA award. G.O. was supported by the Claudia Adams Barr Program for Innovative Cancer Research and by DF/HCC Kidney Cancer SPORE P50 CA101942. S.L. is supported by the National Institutes of Health, National Cancer Institute Research Specialist Award (R50CA251956). JSG is supported by the Conquer Cancer Foundation Career Development Award, Leukemia and Lymphoma Society Translational Research Program Award, and NIH K08CA245209. NCI CTEP provided study drug (Ipilimumab) support. This work was further supported by the CIMAC-CIDC Network. Scientific and financial support for the CIMAC-CIDC Network is provided through National Institutes of Health, National Cancer Institute Cooperative Agreements U24CA224319 (to the Icahn School of Medicine at Mount Sinai CIMAC), U24CA224331 (to the Dana-Farber Cancer Institute CIMAC), U24CA224285 (to the MD Anderson Cancer Center CIMAC), U24CA224309 (to the Stanford University CIMAC), and U24CA224316 (to the CIDC at Dana-Farber Cancer Institute). The CIMAC-CIDC website is found at https://cimac-network.org/.
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Affiliation(s)
- Livius Penter
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Hematology, Oncology, and Tumorimmunology, Campus Virchow Klinikum, Berlin, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, BIH Biomedical Innovation Academy, BIH Charité Digital Clinician Scientist Program, Charitéplatz 1, 10117, Berlin, Germany
| | - Mehdi Borji
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Adi Nagler
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Haoxiang Lyu
- Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Wesley S Lu
- Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Nicoletta Cieri
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Katie Maurer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Giacomo Oliveira
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Aziz M Al'Khafaji
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Kiran V Garimella
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Shuqiang Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Donna S Neuberg
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jerome Ritz
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Robert J Soiffer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Jacqueline S Garcia
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Kenneth J Livak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Catherine J Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.
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11
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Xiao Z, Liu X, Kang X, Feng Y, Zheng L, Chen C. Rapid and accurate detection of SARS-CoV-2 using the RHAM technology. Sci Rep 2023; 13:22798. [PMID: 38129524 PMCID: PMC10739982 DOI: 10.1038/s41598-023-49733-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 12/11/2023] [Indexed: 12/23/2023] Open
Abstract
Rapid and sensitive detection of pathogens is of utmost importance in interrupting the transmission chain of infectious diseases. In recent years, this has proven to be vital during the coronavirus disease (COVID-19) global pandemic that put countless lives at risk. Numerous molecular diagnostic methods were used, including RT-PCR, NASBA, E-SDA, E-RCA, LAMP, and RPA. However, these technologies potentially require primer optimization and complex instruments. Here, we propose the RHAM (RNase Hybridization-Assisted amplification) system as a rapid, specific, and sensitive molecular diagnosis platform. Combining the LAMP and RNase HII-mediated fluorescent reporter, the RHAM system can amplify and visualize the target in one isothermal system with high sensitivity (5 × 102 copies/mL). There was no cross-reactivity with other common respiratory viruses. Analysis of clinical samples revealed the RHAM system to generate positive signals within 15 min without false positive or negative results. The present study shows that RHAM is not only an ideal platform for detecting pathogens, such as SARS-CoV-2 but can be potentially applied in POCT settings.
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Affiliation(s)
- Zhuo Xiao
- Guangzhou Pluslife Biotech Co., Ltd., No. 6 Lianhuayan Road, Huangpu District, Guangzhou, 510700, Guangdong, China
| | - Xiaoli Liu
- Guangzhou Pluslife Biotech Co., Ltd., No. 6 Lianhuayan Road, Huangpu District, Guangzhou, 510700, Guangdong, China
| | - Xiaolong Kang
- Guangzhou Pluslife Biotech Co., Ltd., No. 6 Lianhuayan Road, Huangpu District, Guangzhou, 510700, Guangdong, China
| | - Yaoheng Feng
- Guangzhou Pluslife Biotech Co., Ltd., No. 6 Lianhuayan Road, Huangpu District, Guangzhou, 510700, Guangdong, China
| | - Lijun Zheng
- Guangzhou Pluslife Biotech Co., Ltd., No. 6 Lianhuayan Road, Huangpu District, Guangzhou, 510700, Guangdong, China
| | - Chong Chen
- Guangzhou Pluslife Biotech Co., Ltd., No. 6 Lianhuayan Road, Huangpu District, Guangzhou, 510700, Guangdong, China.
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12
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Yao J, Zhang Z, Tian S, Luo N, Tan J, Zhang Y, Gu S, Xia Q. Synchronous detection of Burkholderia pseudomallei and its ceftazidime resistance mutation based on RNase-HII hydrolysis combined with lateral flow strip assay. Microbiol Spectr 2023; 11:e0112523. [PMID: 37815337 PMCID: PMC10714834 DOI: 10.1128/spectrum.01125-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 08/19/2023] [Indexed: 10/11/2023] Open
Abstract
IMPORTANCE This study focused on the development of a reaction system using rhPCR to amplify a specific gene, ORF2, of B. pseudomallei and to identify the P174L mutation associated with increased drug resistance to ceftazidime (CAZ). The system incorporated universal primer probes and a simple temperature cycle reaction. The amplified products were then analyzed using lateral flow strip assay (LFSA) for strain identification and mutation interpretation. The developed system provides a reliable basis for diagnosing melioidosis and selecting appropriate drugs. Its potential impact is particularly significant in resource-limited settings where access to advanced diagnostic techniques is limited. This platform stands out for its simplicity, convenience, sensitivity, specificity, and portability. It shows promise as a point-of-care testing method for detecting single nucleotide polymorphism in genes associated with other diseases. By leveraging the advantages of this platform, researchers and healthcare professionals can potentially expand its use beyond melioidosis and apply it to the rapid detection of genetic variations in other disease-related genes.
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Affiliation(s)
- Juan Yao
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, NHC Key Laboratory of Tropical Disease Control, School of Tropical Medicine, Hainan Medical University, Haikou, Hainan, China
- Nanobiosensing and Microfluidic Point-of-Care Testing Key Laboratory of LuZhou, Luzhou, Sichuan, China
| | - Zhang Zhang
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, NHC Key Laboratory of Tropical Disease Control, School of Tropical Medicine, Hainan Medical University, Haikou, Hainan, China
- Department of Neurosurgery, Neurology Center, The First Affiliated Hospital of Hainan Medical University, Haikou, Hainan, China
| | - Shen Tian
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, NHC Key Laboratory of Tropical Disease Control, School of Tropical Medicine, Hainan Medical University, Haikou, Hainan, China
| | - Nini Luo
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, NHC Key Laboratory of Tropical Disease Control, School of Tropical Medicine, Hainan Medical University, Haikou, Hainan, China
| | - Jun Tan
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, NHC Key Laboratory of Tropical Disease Control, School of Tropical Medicine, Hainan Medical University, Haikou, Hainan, China
| | - Yue Zhang
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, NHC Key Laboratory of Tropical Disease Control, School of Tropical Medicine, Hainan Medical University, Haikou, Hainan, China
| | - Shuo Gu
- Department of Neurosurgery, Neurology Center, The First Affiliated Hospital of Hainan Medical University, Haikou, Hainan, China
| | - Qianfeng Xia
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, NHC Key Laboratory of Tropical Disease Control, School of Tropical Medicine, Hainan Medical University, Haikou, Hainan, China
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13
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Edri A, Ben-Haim N, Hailu A, Brycman N, Berhani-Zipori O, Rifman J, Cohen S, Yackoubov D, Rosenberg M, Simantov R, Teru H, Kurata K, Anderson KC, Hendel A, Pato A, Geffen Y. Nicotinamide-Expanded Allogeneic Natural Killer Cells with CD38 Deletion, Expressing an Enhanced CD38 Chimeric Antigen Receptor, Target Multiple Myeloma Cells. Int J Mol Sci 2023; 24:17231. [PMID: 38139060 PMCID: PMC10743602 DOI: 10.3390/ijms242417231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 12/01/2023] [Accepted: 12/01/2023] [Indexed: 12/24/2023] Open
Abstract
Natural killer (NK) cells are a vital component of cancer immune surveillance. They provide a rapid and potent immune response, including direct cytotoxicity and mobilization of the immune system, without the need for antigen processing and presentation. NK cells may also be better tolerated than T cell therapy approaches and are susceptible to various gene manipulations. Therefore, NK cells have become the focus of extensive translational research. Gamida Cell's nicotinamide (NAM) platform for cultured NK cells provides an opportunity to enhance the therapeutic potential of NK cells. CD38 is an ectoenzyme ubiquitously expressed on the surface of various hematologic cells, including multiple myeloma (MM). It has been selected as a lead target for numerous monoclonal therapeutic antibodies against MM. Monoclonal antibodies target CD38, resulting in the lysis of MM plasma cells through various antibody-mediated mechanisms such as antibody-dependent cellular cytotoxicity (ADCC), complement-dependent cytotoxicity, and antibody-dependent cellular phagocytosis, significantly improving the outcomes of patients with relapsed or refractory MM. However, this therapeutic strategy has inherent limitations, such as the anti-CD38-induced depletion of CD38-expressing NK cells, thus hindering ADCC. We have developed genetically engineered NK cells tailored to treat MM, in which CD38 was knocked-out using CRISPR-Cas9 technology and an enhanced chimeric antigen receptor (CAR) targeting CD38 was introduced using mRNA electroporation. This combined genetic approach allows for an improved cytotoxic activity directed against CD38-expressing MM cells without self-inflicted NK-cell-mediated fratricide. Preliminary results show near-complete abolition of fratricide with a 24-fold reduction in self-lysis from 19% in mock-transfected and untreated NK cells to 0.8% of self-lysis in CD38 knock-out CAR NK cells. Furthermore, we have observed significant enhancements in CD38-mediated activity in vitro, resulting in increased lysis of MM target cell lines. CD38 knock-out CAR NK cells also demonstrated significantly higher levels of NK activation markers in co-cultures with both untreated and αCD38-treated MM cell lines. These NAM-cultured NK cells with the combined genetic approach of CD38 knockout and addition of CD38 CAR represent a promising immunotherapeutic tool to target MM.
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Affiliation(s)
- Avishay Edri
- Gamida-Cell, Jerusalem 34670, Israel; (A.E.); (A.H.); (N.B.); (O.B.-Z.); (J.R.); (S.C.); (D.Y.); (A.P.)
| | - Nimrod Ben-Haim
- Institute of Nanotechnology and Advanced Materials, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel; (N.B.-H.); (M.R.)
| | - Astar Hailu
- Gamida-Cell, Jerusalem 34670, Israel; (A.E.); (A.H.); (N.B.); (O.B.-Z.); (J.R.); (S.C.); (D.Y.); (A.P.)
| | - Nurit Brycman
- Gamida-Cell, Jerusalem 34670, Israel; (A.E.); (A.H.); (N.B.); (O.B.-Z.); (J.R.); (S.C.); (D.Y.); (A.P.)
| | - Orit Berhani-Zipori
- Gamida-Cell, Jerusalem 34670, Israel; (A.E.); (A.H.); (N.B.); (O.B.-Z.); (J.R.); (S.C.); (D.Y.); (A.P.)
| | - Julia Rifman
- Gamida-Cell, Jerusalem 34670, Israel; (A.E.); (A.H.); (N.B.); (O.B.-Z.); (J.R.); (S.C.); (D.Y.); (A.P.)
| | - Sherri Cohen
- Gamida-Cell, Jerusalem 34670, Israel; (A.E.); (A.H.); (N.B.); (O.B.-Z.); (J.R.); (S.C.); (D.Y.); (A.P.)
| | - Dima Yackoubov
- Gamida-Cell, Jerusalem 34670, Israel; (A.E.); (A.H.); (N.B.); (O.B.-Z.); (J.R.); (S.C.); (D.Y.); (A.P.)
| | - Michael Rosenberg
- Institute of Nanotechnology and Advanced Materials, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel; (N.B.-H.); (M.R.)
| | | | - Hideshima Teru
- Jerome Lipper Multiple Myeloma Center, LeBow Institute for Myeloma Therapeutics, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; (H.T.); (K.K.); (K.C.A.)
| | - Keiji Kurata
- Jerome Lipper Multiple Myeloma Center, LeBow Institute for Myeloma Therapeutics, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; (H.T.); (K.K.); (K.C.A.)
| | - Kenneth Carl Anderson
- Jerome Lipper Multiple Myeloma Center, LeBow Institute for Myeloma Therapeutics, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; (H.T.); (K.K.); (K.C.A.)
| | - Ayal Hendel
- Institute of Nanotechnology and Advanced Materials, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel; (N.B.-H.); (M.R.)
| | - Aviad Pato
- Gamida-Cell, Jerusalem 34670, Israel; (A.E.); (A.H.); (N.B.); (O.B.-Z.); (J.R.); (S.C.); (D.Y.); (A.P.)
| | - Yona Geffen
- Gamida-Cell, Jerusalem 34670, Israel; (A.E.); (A.H.); (N.B.); (O.B.-Z.); (J.R.); (S.C.); (D.Y.); (A.P.)
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14
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Song Z, Hu K, Rao J, Cheng B, Xu L, An R, Liang X. Unexpected Mechanism and Inhibition Effect for Nonspecific Amplification Involving Dynamic Binding of Primers with Background DNA. Anal Chem 2023; 95:16819-16829. [PMID: 37922263 DOI: 10.1021/acs.analchem.3c02274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2023]
Abstract
Nonspecific amplification is a serious issue in DNA detection as it can lead to false-positive results and reduce specificity. It is very important to well understand its mechanism through sequencing nonspecific products. Here, an approach is developed using a nanopore sequencing technique after acquiring the long repetitive sequence of DNA products from nonspecific amplification. Based on the sequencing results, a new mechanism of nonspecific amplification designated as dynamic mismatched primer binding (DMPB) with the background DNA (bgDNA) is proposed. Unexpectedly, our findings show that the primers (∼20 nt) can bind to bgDNA for primer extension when only 6-11 fully matched (9-14 mismatched) base pairs are formed. After the single-stranded DNAs (ssDNAs) attached to the first primer are produced, more interestingly, with the aid of DNA polymerase, the other primer can bind to these ssDNAs in the case that the fully matched base pairs formed between them are even shorter than 6 bp. As a result, perfect "seeds" for polymerase chain reaction with information on both primers are produced so that exponential nonspecific amplification can occur. The DMPB mechanism can explain nonspecific amplification in other approaches as well. Finally, a mini-hairpin DNA is used to effectively inhibit nonspecific amplification by preventing the formation of an unexpected primer-bgDNA complex.
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Affiliation(s)
- Ziting Song
- State Key Laboratory of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao 266404, China
| | - Kunling Hu
- State Key Laboratory of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao 266404, China
| | - Jun Rao
- State Key Laboratory of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao 266404, China
| | - Bingxiao Cheng
- State Key Laboratory of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao 266404, China
| | - Liyuan Xu
- State Key Laboratory of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao 266404, China
| | - Ran An
- State Key Laboratory of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao 266404, China
- Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China
| | - Xingguo Liang
- State Key Laboratory of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao 266404, China
- Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China
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15
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Kang B, Zhang J, Schwoerer MP, Nelson AN, Schoeman E, Guo A, Ploss A, Myhrvold C. Highly multiplexed mRNA quantitation with CRISPR-Cas13. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.16.553527. [PMID: 37645785 PMCID: PMC10461975 DOI: 10.1101/2023.08.16.553527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
RNA quantitation tools are often either high-throughput or cost-effective, but rarely are they both. Existing methods can profile the transcriptome at great expense or are limited to quantifying a handful of genes by labor constraints. A technique that permits more throughput at a reduced cost could enable multi-gene kinetic studies, gene regulatory network analysis, and combinatorial genetic screens. Here, we introduce quantitative Combinatorial Arrayed Reactions for Multiplexed Evaluation of Nucleic acids (qCARMEN): an RNA quantitation technique which leverages the programmable RNA-targeting capabilities of CRISPR-Cas13 to address this challenge by quantifying over 4,500 gene-sample pairs in a single experiment. Using qCARMEN, we studied the response profiles of interferon-stimulated genes (ISGs) during interferon (IFN) stimulation and flavivirus infection. Additionally, we observed isoform switching kinetics during epithelial-mesenchymal transition. qCARMEN is a simple and inexpensive technique that greatly enhances the scalability of RNA quantitation for novel applications with performance similar to gold-standard methods.
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Affiliation(s)
- Brian Kang
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544
| | - Jiayu Zhang
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544
| | | | - Amy N. Nelson
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544
| | - Emily Schoeman
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544
| | - Andrew Guo
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544
| | - Alexander Ploss
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544
| | - Cameron Myhrvold
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544
- Omenn-Darling Bioengineering Institute, Princeton University, Princeton, NJ 08544
- Department of Chemistry, Princeton University, Princeton, NJ 08544
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16
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Zhang Z, Guan L, Yao J, Li L, Liu C, Guo Y, Xie G. RART-LAMP: One-Step Extraction-Free Method for Genotyping within 40 min. Anal Chem 2023; 95:12487-12496. [PMID: 37534990 DOI: 10.1021/acs.analchem.3c02232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/04/2023]
Abstract
Loop-mediated isothermal amplification (LAMP) is a commonly used alternative to PCR for point-of-care detection of nucleic acids due to its rapidity, sensitivity, specificity, and simpler instrumentation. While dual-labeled TaqMan probes are widely used in PCR for single-nucleotide polymorphism (SNP) genotyping, real-time LAMP primarily relies on turbidimetry or intercalator fluorescence measurements, which can be non-specific and generate false-positive results. In this study, we propose a closed-tube, dual-labeled RNA-modified probes and RNase H II-assisted real-time LAMP (RART-LAMP) method for SNP genotyping. Our findings indicate that (1) fluorescence signals were predominantly derived from probe hydrolysis rather than hybridization, (2) temperature-controlled hybridization between the probe and template ensured the specificity of SNP analysis, and (3) RNase H II hydrolysis between the target containing SNP sites and probes did not exhibit sequence specificity. Our RART-LAMP approach demonstrated excellent performance in genotyping C677T clinical samples, including gDNA extracted from blood, saliva, and swabs. More importantly, saliva and swab samples could be directly analyzed without any pretreatment, indicating promising prospects for nucleic acid analysis at the point of care in resource-limited settings.
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Affiliation(s)
- Zhang Zhang
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing 400016, China
| | - Luhao Guan
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing 400016, China
- Department of Laboratory Medicine, Luzhou Traditional Chinese Medicine Hospital, Luzhou 646000, China
| | - Juan Yao
- Department of Laboratory Medicine, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou 646000, China
| | - Lijia Li
- Zhuhai Biori Biotechnology Company Limited, Zhuhai 519000, China
| | - Chunfang Liu
- Zhuhai Biori Biotechnology Company Limited, Zhuhai 519000, China
| | - Yongcan Guo
- Department of Laboratory Medicine, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou 646000, China
| | - Guoming Xie
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing 400016, China
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17
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Liu Z, Pan S, Wu P, Li M, Liang D. Determination of A1 and A2 β-Casein in Milk Using Characteristic Thermolytic Peptides via Liquid Chromatography-Mass Spectrometry. Molecules 2023; 28:5200. [PMID: 37446860 DOI: 10.3390/molecules28135200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 07/02/2023] [Accepted: 07/02/2023] [Indexed: 07/15/2023] Open
Abstract
β-casein, a protein in milk and dairy products, has two main variant forms termed as A1 and A2. A1 β-casein may have adverse effects on humans. The fact that there is only one amino acid variation at the 67th position between A1 and A2 β-casein makes it difficult to distinguish between them. In this study, a novel method using characteristic thermolytic peptides is developed for the determination of A1 and A2 β-casein in milk. Firstly, caseins extracted from milk samples are thermolytic digested at 60 °C without any denaturing reagents required for unfolding proteins, which simplifies the sample pretreatment procedure. The characteristic thermolytic peptides (i.e., fragments 66-76 and 59-76 for A1 and A2 β-casein, respectively) selected to specifically distinguish A1 and A2 β-casein only have eleven or eighteen amino acid moieties. Compared with tryptic characteristic peptides with a length of 49 amino acid moieties, these shorter thermolytic characteristic peptides are more suitable for LC-MS analysis. This novel method, with the advantages of high specificity, high sensitivity, and high efficiency, was successfully applied for the analysis of six milk samples collected from a local supermarket. After further investigation, it is found that this method would contribute to the development of A2 dairy products for a company and the quality inspection of A2 dairy products for a government.
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Affiliation(s)
- Zeyang Liu
- Key Laboratory of Groundwater Resources and Environment of the Ministry of Education, Jilin University, Changchun 130012, China
- Division of Chemical Metrology & Analytical Science, National Institute of Metrology, Beijing 100029, China
| | - Susu Pan
- Division of Ecology Environment and Energy Resources, Beijing Institute of Metrology, Beijing 100012, China
| | - Peize Wu
- Division of Chemical Metrology & Analytical Science, National Institute of Metrology, Beijing 100029, China
| | - Ming Li
- Division of Chemical Metrology & Analytical Science, National Institute of Metrology, Beijing 100029, China
| | - Dapeng Liang
- Key Laboratory of Groundwater Resources and Environment of the Ministry of Education, Jilin University, Changchun 130012, China
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18
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Zeng J, Nguyen MA, Liu P, Ferreira da Silva L, Lin LY, Justus DG, Petri K, Clement K, Porter SN, Verma A, Neri NR, Rosanwo T, Ciuculescu MF, Abriss D, Mintzer E, Maitland SA, Demirci S, Tisdale JF, Williams DA, Zhu LJ, Pruett-Miller SM, Pinello L, Joung JK, Pattanayak V, Manis JP, Armant M, Pellin D, Brendel C, Wolfe SA, Bauer DE. Gene editing without ex vivo culture evades genotoxicity in human hematopoietic stem cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.27.542323. [PMID: 37292647 PMCID: PMC10245949 DOI: 10.1101/2023.05.27.542323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Gene editing the BCL11A erythroid enhancer is a validated approach to fetal hemoglobin (HbF) induction for β-hemoglobinopathy therapy, though heterogeneity in edit allele distribution and HbF response may impact its safety and efficacy. Here we compared combined CRISPR-Cas9 endonuclease editing of the BCL11A +58 and +55 enhancers with leading gene modification approaches under clinical investigation. We found that combined targeting of the BCL11A +58 and +55 enhancers with 3xNLS-SpCas9 and two sgRNAs resulted in superior HbF induction, including in engrafting erythroid cells from sickle cell disease (SCD) patient xenografts, attributable to simultaneous disruption of core half E-box/GATA motifs at both enhancers. We corroborated prior observations that double strand breaks (DSBs) could produce unintended on- target outcomes in hematopoietic stem and progenitor cells (HSPCs) such as long deletions and centromere-distal chromosome fragment loss. We show these unintended outcomes are a byproduct of cellular proliferation stimulated by ex vivo culture. Editing HSPCs without cytokine culture bypassed long deletion and micronuclei formation while preserving efficient on-target editing and engraftment function. These results indicate that nuclease editing of quiescent hematopoietic stem cells (HSCs) limits DSB genotoxicity while maintaining therapeutic potency and encourages efforts for in vivo delivery of nucleases to HSCs.
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Jiang J, Feindel W, Harding M, Feindel D, Bajema S, Feng J. Detection of Ilyonectria pseudodestructans from Potato by RNase H-Dependent PCR (rhPCR) and rh-Quantitative PCR (rhqPCR). PLANT DISEASE 2023:PDIS08221809RE. [PMID: 36383993 DOI: 10.1094/pdis-08-22-1809-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Ilyonectria pseudodestructans, a plant pathogen that is known to cause root rot on fruit trees such as grapevine and apple, has recently been reported to also cause tuber decay in potato. The increasing risk of this pathogen on various horticultural crops makes it essential to develop a rapid and accurate detection method. In this study, an RNase H-dependent PCR (rhPCR) protocol and a modified probe-based rh-quantitative PCR (rhqPCR) protocol for I. pseudodestructans detection were developed. Both the forward and reverse primers for rhPCR and rhqPCR carry an RNA nucleotide at the site where a single-nucleotide polymorphism between I. pseudodestructans and strains of other Ilyonectria spp. is located, and the rhqPCR also contains a fluorescent-labeled target-specific probe. The primers were designed based on the sequence of the histone H3 gene and could amplify a DNA fragment of 73 bp. In the specificity test, by alignment via the BLASTn tool, the RNA nucleotide bases on both the forward and the reverse primers were identical to the corresponding genomic site of 16 of 17 (94.1%) database-available I. pseudodestructans strains, and different from 43 of 44 (97.7%) database-available strains of other Ilyonectria spp. When the rhPCR and rhqPCR protocols were applied on 11 I. pseudodestructans strains and 46 other strains of different species of plant pathogens, all of the I. pseudodestructans strains generated positive reactions whereas all of the other strains were negative, which indicated an excellent specificity of the primers. In the sensitivity test, the lowest DNA template amount for a positive reaction using the rhPCR and rhqPCR methods was 2 pg for I. pseudodestructans genomic DNA. When testing the rhqPCR method on gBlock, the lowest number of molecules for a positive reaction was six. These results indicated a high sensitivity of the protocol for I. pseudodestructans detection. To our knowledge, this is the first report of a probe-based rhqPCR to be applied to plant disease diagnosis; in addition, this is also the first rapid molecular protocol to detect I. pseudodestructans. The new rhPCR and rhqPCR methods have a potential to be applied by plant disease diagnostic labs for their routine work.
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Affiliation(s)
- Junye Jiang
- Potato Growers of Alberta, Edmonton, Alberta T5Y 6H3, Canada
| | - Will Feindel
- Potato Growers of Alberta, Edmonton, Alberta T5Y 6H3, Canada
| | - Michael Harding
- Crop Diversification Centre South, Alberta Agriculture and Irrigation (AGI), Brooks, Alberta T1R 1E6, Canada
| | - David Feindel
- Alberta Plant Health Lab, AGI, Edmonton, Alberta T5Y 6H3, Canada
| | - Stacey Bajema
- Potato Growers of Alberta, Edmonton, Alberta T5Y 6H3, Canada
| | - Jie Feng
- Alberta Plant Health Lab, AGI, Edmonton, Alberta T5Y 6H3, Canada
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20
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Hung YP, Chebib I, Bredella MA, Berner EA, Taylor-Black Q, Choy E, Cote GM, Chen YL, MacDonald SM, Schwab JH, Raskin KA, Newman ET, Selig MK, Deshpande V, Hornick JL, Lozano-Calderón SA, Nielsen GP. Prognostic Significance of Percentage and Size of Dedifferentiation in Dedifferentiated Chondrosarcoma. Mod Pathol 2023; 36:100069. [PMID: 36788104 DOI: 10.1016/j.modpat.2022.100069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 11/17/2022] [Accepted: 12/11/2022] [Indexed: 01/11/2023]
Abstract
Dedifferentiated chondrosarcoma is rare, aggressive, and microscopically bimorphic. How pathologic features such as the amounts of dedifferentiation affect prognosis remains unclear. We evaluated the percentages and sizes of dedifferentiation in a consecutive institutional series of dedifferentiated chondrosarcomas from 1999 to 2021. The statistical analysis included cox proportional hazard models and log-rank tests. Of the 67 patients (26 women, 41 men; age, 39 to >89 [median 61] years; 2 with Ollier disease), 58 presented de novo; 9 were identified with conventional chondrosarcomas 0.6-13.2 years (median, 5.5 years) prior. Pathologic fracture and distant metastases were noted in 27 and 7 patients at presentation. The tumors involved the femur (n = 27), pelvis (n = 22), humerus (n = 7), tibia (n = 4), scapula/ribs (n = 4), spine (n = 2), and clivus (n = 1). In the 56 resections, the tumors ranged in size from 3.5 to 46.0 cm (median, 11.5 cm) and contained 1%-99.5% (median, 70%) dedifferentiated components that ranged in size from 0.6 to 24.0 cm (median, 7.3 cm). No correlation was noted between total size and percentage of dedifferentiation. The dedifferentiated components were typically fibrosarcomatous or osteosarcomatous, whereas the associated cartilaginous components were predominantly grade 1-2, rarely enchondromas or grade 3. The entire cohort's median overall survival and progression-free survival were 11.8 and 5.4 months, respectively. In the resected cohort, although the total size was not prognostic, the percentage of dedifferentiation ≥20% and size of dedifferentiation >3.0 cm each predicted worse overall survival (9.9 vs 72.5 months; HR, 3.76; 95% CI, 1.27-11.14; P = .02; 8.7 vs 58.9 months; HR, 3.03; 95% CI, 1.21-7.57; P = .02, respectively) and progression-free survival (5.3 vs 62.1 months; HR, 3.05; 95% CI, 1.13-8.28; P = .03; 5.3 vs 56.6 months; HR, 2.50; 95% CI, 1.06-5.88; P = .04, respectively). In conclusion, both the percentages and sizes of dedifferentiation were better prognostic predictors than total tumor sizes in dedifferentiated chondrosarcomas, highlighting the utility of their pathologic evaluations.
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Affiliation(s)
- Yin P Hung
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts; Center for Sarcoma and Connective Tissue Oncology, Massachusetts General Hospital Cancer Center, Boston, Massachusetts.
| | - Ivan Chebib
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts; Center for Sarcoma and Connective Tissue Oncology, Massachusetts General Hospital Cancer Center, Boston, Massachusetts
| | - Miriam A Bredella
- Center for Sarcoma and Connective Tissue Oncology, Massachusetts General Hospital Cancer Center, Boston, Massachusetts; Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Emily A Berner
- Department of Orthopedic Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Quinn Taylor-Black
- Department of Orthopedic Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Edwin Choy
- Center for Sarcoma and Connective Tissue Oncology, Massachusetts General Hospital Cancer Center, Boston, Massachusetts; Division of Hematology Oncology, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Gregory M Cote
- Center for Sarcoma and Connective Tissue Oncology, Massachusetts General Hospital Cancer Center, Boston, Massachusetts; Division of Hematology Oncology, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Yen-Lin Chen
- Center for Sarcoma and Connective Tissue Oncology, Massachusetts General Hospital Cancer Center, Boston, Massachusetts; Department of Radiation Oncology, Massachusetts General Hospital, Boston, Massachusetts
| | - Shannon M MacDonald
- Center for Sarcoma and Connective Tissue Oncology, Massachusetts General Hospital Cancer Center, Boston, Massachusetts; Department of Radiation Oncology, Massachusetts General Hospital, Boston, Massachusetts
| | - Joseph H Schwab
- Center for Sarcoma and Connective Tissue Oncology, Massachusetts General Hospital Cancer Center, Boston, Massachusetts; Department of Orthopedic Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Kevin A Raskin
- Center for Sarcoma and Connective Tissue Oncology, Massachusetts General Hospital Cancer Center, Boston, Massachusetts; Department of Orthopedic Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Erik T Newman
- Center for Sarcoma and Connective Tissue Oncology, Massachusetts General Hospital Cancer Center, Boston, Massachusetts; Department of Orthopedic Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Martin K Selig
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Vikram Deshpande
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts; Center for Sarcoma and Connective Tissue Oncology, Massachusetts General Hospital Cancer Center, Boston, Massachusetts
| | - Jason L Hornick
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Santiago A Lozano-Calderón
- Center for Sarcoma and Connective Tissue Oncology, Massachusetts General Hospital Cancer Center, Boston, Massachusetts; Department of Orthopedic Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - G Petur Nielsen
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts; Center for Sarcoma and Connective Tissue Oncology, Massachusetts General Hospital Cancer Center, Boston, Massachusetts
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21
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Brault J, Liu T, Liu S, Lawson A, Choi U, Kozhushko N, Bzhilyanskaya V, Pavel-Dinu M, Meis RJ, Eckhaus MA, Burkett SS, Bosticardo M, Kleinstiver BP, Notarangelo LD, Lazzarotto CR, Tsai SQ, Wu X, Dahl GA, Porteus MH, Malech HL, De Ravin SS. CRISPR-Cas9-AAV versus lentivector transduction for genome modification of X-linked severe combined immunodeficiency hematopoietic stem cells. Front Immunol 2023; 13:1067417. [PMID: 36685559 PMCID: PMC9846165 DOI: 10.3389/fimmu.2022.1067417] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 12/06/2022] [Indexed: 01/05/2023] Open
Abstract
Introduction Ex vivo gene therapy for treatment of Inborn errors of Immunity (IEIs) have demonstrated significant clinical benefit in multiple Phase I/II clinical trials. Current approaches rely on engineered retroviral vectors to randomly integrate copy(s) of gene-of-interest in autologous hematopoietic stem/progenitor cells (HSPCs) genome permanently to provide gene function in transduced HSPCs and their progenies. To circumvent concerns related to potential genotoxicities due to the random vector integrations in HSPCs, targeted correction with CRISPR-Cas9-based genome editing offers improved precision for functional correction of multiple IEIs. Methods We compare the two approaches for integration of IL2RG transgene for functional correction of HSPCs from patients with X-linked Severe Combined Immunodeficiency (SCID-X1 or XSCID); delivery via current clinical lentivector (LV)-IL2RG versus targeted insertion (TI) of IL2RG via homology-directed repair (HDR) when using an adeno-associated virus (AAV)-IL2RG donor following double-strand DNA break at the endogenous IL2RG locus. Results and discussion In vitro differentiation of LV- or TI-treated XSCID HSPCs similarly overcome differentiation block into Pre-T-I and Pre-T-II lymphocytes but we observed significantly superior development of NK cells when corrected by TI (40.7% versus 4.1%, p = 0.0099). Transplants into immunodeficient mice demonstrated robust engraftment (8.1% and 23.3% in bone marrow) for LV- and TI-IL2RG HSPCs with efficient T cell development following TI-IL2RG in all four patients' HSPCs. Extensive specificity analysis of CRISPR-Cas9 editing with rhAmpSeq covering 82 predicted off-target sites found no evidence of indels in edited cells before (in vitro) or following transplant, in stark contrast to LV's non-targeted vector integration sites. Together, the improved efficiency and safety of IL2RG correction via CRISPR-Cas9-based TI approach provides a strong rationale for a clinical trial for treatment of XSCID patients.
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Affiliation(s)
- Julie Brault
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Taylor Liu
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Siyuan Liu
- Cancer Research Technology Program, Leidos Biomedical Research Inc., Frederick, MD, United States
| | - Amanda Lawson
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Uimook Choi
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Nikita Kozhushko
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Vera Bzhilyanskaya
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Mara Pavel-Dinu
- Department of Pediatrics, Division of Stem Cell Transplantation and Regenerative Medicine, Stanford University, Palo Alto, CA, United States
| | | | - Michael A. Eckhaus
- Division of Veterinary Resources, Office of Research Services, National Institutes of Health, Bethesda, MD, United States
| | - Sandra S. Burkett
- Molecular Cytogenetic Core Facility, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, United States
| | - Marita Bosticardo
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Benjamin P. Kleinstiver
- Center for Genomic Medicine and Department of Pathology, Massachusetts General Hospital, Boston, MA, United States
- Department of Pathology, Harvard Medical School, Boston, MA, United States
| | - Luigi D. Notarangelo
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Cicera R. Lazzarotto
- Department of Hematology, St. Jude Children’s Research Hospital, Memphis, TN, United States
| | - Shengdar Q. Tsai
- Department of Hematology, St. Jude Children’s Research Hospital, Memphis, TN, United States
| | - Xiaolin Wu
- Cancer Research Technology Program, Leidos Biomedical Research Inc., Frederick, MD, United States
| | | | - Matthew H. Porteus
- Department of Pediatrics, Division of Stem Cell Transplantation and Regenerative Medicine, Stanford University, Palo Alto, CA, United States
| | - Harry L. Malech
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Suk See De Ravin
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, United States
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22
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Gao Y, Sridhar A, Bernard N, He B, Zhang H, Pirotte S, Desmecht S, Vancsok C, Boutier M, Suárez NM, Davison AJ, Donohoe O, Vanderplasschen AFC. Virus-induced interference as a means for accelerating fitness-based selection of cyprinid herpesvirus 3 single-nucleotide variants in vitro and in vivo. Virus Evol 2023; 9:vead003. [PMID: 36816049 PMCID: PMC9936792 DOI: 10.1093/ve/vead003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 12/16/2022] [Accepted: 01/16/2023] [Indexed: 01/19/2023] Open
Abstract
Cyprinid herpesvirus 3 (CyHV-3) is the archetype of fish alloherpesviruses and is advantageous to research because, unlike many herpesviruses, it can be studied in the laboratory by infection of the natural host (common and koi carp). Previous studies have reported a negative correlation among CyHV-3 strains between viral growth in vitro (in cell culture) and virulence in vivo (in fish). This suggests the existence of genovariants conferring enhanced fitness in vitro but reduced fitness in vivo and vice versa. Here, we identified the syncytial plaque formation in vitro as a common trait of CyHV-3 strains adapted to cell culture. A comparison of the sequences of virion transmembrane protein genes in CyHV-3 strains, and the use of various recombinant viruses, demonstrated that this trait is linked to a single-nucleotide polymorphism (SNP) in the open reading frame (ORF) 131 coding sequence (C225791T mutation) that results in codon 183 encoding either an alanine (183A) or a threonine (183T) residue. In experiments involving infections with recombinant viruses differing only by this SNP, the 183A genovariant associated with syncytial plaque formation was the more fit in vitro but the less fit in vivo. In experiments involving coinfection with both viruses, the more fit genovariant contributed to the purifying selection of the less fit genovariant by outcompeting it. In addition, this process appeared to be accelerated by viral stimulation of interference at a cellular level and stimulation of resistance to superinfection at a host level. Collectively, this study illustrates how the fundamental biological properties of some viruses and their hosts may have a profound impact on the degree of diversity that arises within viral populations.
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Affiliation(s)
- Yuan Gao
- Immunology-Vaccinology, Department of Infectious and Parasitic Diseases, Fundamental and Applied Research for Animals & Health (FARAH), Faculty of Veterinary Medicine, University of Liège, Liège B-4000, Belgium
| | - Arun Sridhar
- Immunology-Vaccinology, Department of Infectious and Parasitic Diseases, Fundamental and Applied Research for Animals & Health (FARAH), Faculty of Veterinary Medicine, University of Liège, Liège B-4000, Belgium
| | - Noah Bernard
- Immunology-Vaccinology, Department of Infectious and Parasitic Diseases, Fundamental and Applied Research for Animals & Health (FARAH), Faculty of Veterinary Medicine, University of Liège, Liège B-4000, Belgium
| | - Bo He
- Immunology-Vaccinology, Department of Infectious and Parasitic Diseases, Fundamental and Applied Research for Animals & Health (FARAH), Faculty of Veterinary Medicine, University of Liège, Liège B-4000, Belgium
| | - Haiyan Zhang
- Immunology-Vaccinology, Department of Infectious and Parasitic Diseases, Fundamental and Applied Research for Animals & Health (FARAH), Faculty of Veterinary Medicine, University of Liège, Liège B-4000, Belgium
| | - Sébastien Pirotte
- Immunology-Vaccinology, Department of Infectious and Parasitic Diseases, Fundamental and Applied Research for Animals & Health (FARAH), Faculty of Veterinary Medicine, University of Liège, Liège B-4000, Belgium
| | - Salomé Desmecht
- Laboratory of Animal Genomics, GIGA-Medical Genomics, GIGA-Institute, University of Liège, Liège B-4000, Belgium
| | - Catherine Vancsok
- Immunology-Vaccinology, Department of Infectious and Parasitic Diseases, Fundamental and Applied Research for Animals & Health (FARAH), Faculty of Veterinary Medicine, University of Liège, Liège B-4000, Belgium
| | - Maxime Boutier
- Immunology-Vaccinology, Department of Infectious and Parasitic Diseases, Fundamental and Applied Research for Animals & Health (FARAH), Faculty of Veterinary Medicine, University of Liège, Liège B-4000, Belgium
| | - Nicolás M Suárez
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
| | - Andrew J Davison
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
| | - Owen Donohoe
- Immunology-Vaccinology, Department of Infectious and Parasitic Diseases, Fundamental and Applied Research for Animals & Health (FARAH), Faculty of Veterinary Medicine, University of Liège, Liège B-4000, Belgium.,Bioscience Research Institute, Technological University of the Shannon, Midlands Midwest, Athlone, Co. Westmeath N37HD68, Ireland
| | - Alain F C Vanderplasschen
- Immunology-Vaccinology, Department of Infectious and Parasitic Diseases, Fundamental and Applied Research for Animals & Health (FARAH), Faculty of Veterinary Medicine, University of Liège, Liège B-4000, Belgium
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23
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Biederstädt A, Manzar GS, Daher M. Multiplexed engineering and precision gene editing in cellular immunotherapy. Front Immunol 2022; 13:1063303. [PMID: 36483551 PMCID: PMC9723254 DOI: 10.3389/fimmu.2022.1063303] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 10/31/2022] [Indexed: 11/23/2022] Open
Abstract
The advent of cellular immunotherapy in the clinic has entirely redrawn the treatment landscape for a growing number of human cancers. Genetically reprogrammed immune cells, including chimeric antigen receptor (CAR)-modified immune effector cells as well as T cell receptor (TCR) therapy, have demonstrated remarkable responses across different hard-to-treat patient populations. While these novel treatment options have had tremendous success in providing long-term remissions for a considerable fraction of treated patients, a number of challenges remain. Limited in vivo persistence and functional exhaustion of infused immune cells as well as tumor immune escape and on-target off-tumor toxicities are just some examples of the challenges which restrain the potency of today's genetically engineered cell products. Multiple engineering strategies are being explored to tackle these challenges.The advent of multiplexed precision genome editing has in recent years provided a flexible and highly modular toolkit to specifically address some of these challenges by targeted genetic interventions. This class of next-generation cellular therapeutics aims to endow engineered immune cells with enhanced functionality and shield them from immunosuppressive cues arising from intrinsic immune checkpoints as well as the hostile tumor microenvironment (TME). Previous efforts to introduce additional genetic modifications into immune cells have in large parts focused on nuclease-based tools like the CRISPR/Cas9 system or TALEN. However, nuclease-inactive platforms including base and prime editors have recently emerged and promise a potentially safer route to rewriting genetic sequences and introducing large segments of transgenic DNA without inducing double-strand breaks (DSBs). In this review, we discuss how these two exciting and emerging fields-cellular immunotherapy and precision genome editing-have co-evolved to enable a dramatic expansion in the possibilities to engineer personalized anti-cancer treatments. We will lay out how various engineering strategies in addition to nuclease-dependent and nuclease-inactive precision genome editing toolkits are increasingly being applied to overcome today's limitations to build more potent cellular therapeutics. We will reflect on how novel information-rich unbiased discovery approaches are continuously deepening our understanding of fundamental mechanisms governing tumor biology. We will conclude with a perspective of how multiplexed-engineered and gene edited cell products may upend today's treatment paradigms as they evolve into the next generation of more potent cellular immunotherapies.
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Affiliation(s)
- Alexander Biederstädt
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
- Department of Medicine III, Hematology and Oncology, School of Medicine, Technical University of Munich, Munich, Germany
| | - Gohar Shahwar Manzar
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - May Daher
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
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24
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Meng J, Li C, Wang Y, Bian Z, Chu P, Zhai S, Yang D, Song S, Li Y, Jiang Z, Zhang K, Li Y, Gou H. Accelerated loop-mediated isothermal amplification method for the rapid detection of Streptococcus suis serotypes 2 and 14 based on single nucleotide polymorphisms. Front Cell Infect Microbiol 2022; 12:1034762. [PMID: 36439234 PMCID: PMC9691836 DOI: 10.3389/fcimb.2022.1034762] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 10/21/2022] [Indexed: 11/13/2022] Open
Abstract
Streptococcus suis serotypes 2 and 14 are the most prevalent zoonotic strains. The establishment of a sensitive and extremely accurate method for point-of-care testing for Streptococcus suis serotype 2 and 14 strains is highly desirable. In this study, a loop primer probe-introduced loop-mediated isothermal amplification assay was developed to differentiate Streptococcus suis serotypes 2 and 14 based on SNP (single nucleotide polymorphism). The specific fluorescent probes were designed for the SNP site specific for serotype 2 and 14 Streptococcus suis cpsK genes, and the loop primer probe-introduced loop-mediated isothermal amplification (LAMP) assay was developed using the specific cleavage properties of the RNase H2 enzyme. Rapid and efficient LAMP assays were realized through the use of loop forward primers and stem forward primers. The results showed that the amplification reaction can be performed efficiently at 59°C. The results can be real-time detected or judged using a smartphone and a 3D-printed visualization cassette. The sensitivity of the LAMP assay can reach 18.4 CFU within 40 minutes. The detection rate of the assay system was evaluated using 19 clinical samples with suspected Streptococcus suis infection, and the detection rate was consistent with the sequencing method, suggesting that the test is highly practical. The LAMP assay for Streptococcus suis serotypes 2 and 14 established in this study has strong specificity, high sensitivity, and simple operation, while the reaction can be performed at an isothermal temperature and is not dependent on complex instruments or professional operators, making it suitable for field testing.
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Affiliation(s)
- Jiajia Meng
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Chunling Li
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Livestock Disease Prevention, Guangzhou, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China
- Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Guangzhou, China
| | - Yu Wang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Zhibiao Bian
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Livestock Disease Prevention, Guangzhou, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China
- Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Guangzhou, China
| | - Pinpin Chu
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Livestock Disease Prevention, Guangzhou, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China
- Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Guangzhou, China
| | - Shaolun Zhai
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Livestock Disease Prevention, Guangzhou, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China
- Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Guangzhou, China
| | - Dongxia Yang
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Livestock Disease Prevention, Guangzhou, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China
- Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Guangzhou, China
| | - Shuai Song
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Livestock Disease Prevention, Guangzhou, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China
- Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Guangzhou, China
| | - Yan Li
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Livestock Disease Prevention, Guangzhou, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China
- Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Guangzhou, China
| | - Zhiyong Jiang
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Livestock Disease Prevention, Guangzhou, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China
- Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Guangzhou, China
| | - Kunli Zhang
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Livestock Disease Prevention, Guangzhou, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China
- Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Guangzhou, China
| | - Yugu Li
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- *Correspondence: Yugu Li, ; Hongchao Gou,
| | - Hongchao Gou
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Livestock Disease Prevention, Guangzhou, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China
- Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Guangzhou, China
- *Correspondence: Yugu Li, ; Hongchao Gou,
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25
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Liu S, Iorgulescu JB, Li S, Borji M, Barrera-Lopez IA, Shanmugam V, Lyu H, Morriss JW, Garcia ZN, Murray E, Reardon DA, Yoon CH, Braun DA, Livak KJ, Wu CJ, Chen F. Spatial maps of T cell receptors and transcriptomes reveal distinct immune niches and interactions in the adaptive immune response. Immunity 2022; 55:1940-1952.e5. [PMID: 36223726 PMCID: PMC9745674 DOI: 10.1016/j.immuni.2022.09.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 06/21/2022] [Accepted: 08/31/2022] [Indexed: 12/15/2022]
Abstract
T cells mediate antigen-specific immune responses to disease through the specificity and diversity of their clonotypic T cell receptors (TCRs). Determining the spatial distributions of T cell clonotypes in tissues is essential to understanding T cell behavior, but spatial sequencing methods remain unable to profile the TCR repertoire. Here, we developed Slide-TCR-seq, a 10-μm-resolution method, to sequence whole transcriptomes and TCRs within intact tissues. We confirmed the ability of Slide-TCR-seq to map the characteristic locations of T cells and their receptors in mouse spleen. In human lymphoid germinal centers, we identified spatially distinct TCR repertoires. Profiling T cells in renal cell carcinoma and melanoma specimens revealed heterogeneous immune responses: T cell states and infiltration differed intra- and inter-clonally, and adjacent tumor and immune cells exhibited distinct gene expression. Altogether, our method yields insights into the spatial relationships between clonality, neighboring cell types, and gene expression that drive T cell responses.
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Affiliation(s)
- Sophia Liu
- Biophysics Program, Harvard University, Boston, MA 02115, USA; Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - J Bryan Iorgulescu
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Shuqiang Li
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Mehdi Borji
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | | | - Vignesh Shanmugam
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Haoxiang Lyu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Julia W Morriss
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Zoe N Garcia
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Evan Murray
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - David A Reardon
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Charles H Yoon
- Department of Surgical Oncology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - David A Braun
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Yale Center of Cellular and Molecular Oncology, Yale School of Medicine, New Haven, CT 06511, USA
| | - Kenneth J Livak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Catherine J Wu
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Division of Stem Cell Transplantation and Cellular Therapies, Dana-Farber Cancer Institute, Boston, MA 02215, USA.
| | - Fei Chen
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA.
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26
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Abstract
Natural killer (NK) cells comprise a unique population of innate lymphoid cells endowed with intrinsic abilities to identify and eliminate virally infected cells and tumour cells. Possessing multiple cytotoxicity mechanisms and the ability to modulate the immune response through cytokine production, NK cells play a pivotal role in anticancer immunity. This role was elucidated nearly two decades ago, when NK cells, used as immunotherapeutic agents, showed safety and efficacy in the treatment of patients with advanced-stage leukaemia. In recent years, following the paradigm-shifting successes of chimeric antigen receptor (CAR)-engineered adoptive T cell therapy and the advancement in technologies that can turn cells into powerful antitumour weapons, the interest in NK cells as a candidate for immunotherapy has grown exponentially. Strategies for the development of NK cell-based therapies focus on enhancing NK cell potency and persistence through co-stimulatory signalling, checkpoint inhibition and cytokine armouring, and aim to redirect NK cell specificity to the tumour through expression of CAR or the use of engager molecules. In the clinic, the first generation of NK cell therapies have delivered promising results, showing encouraging efficacy and remarkable safety, thus driving great enthusiasm for continued innovation. In this Review, we describe the various approaches to augment NK cell cytotoxicity and longevity, evaluate challenges and opportunities, and reflect on how lessons learned from the clinic will guide the design of next-generation NK cell products that will address the unique complexities of each cancer.
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Affiliation(s)
- Tamara J Laskowski
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas, MD Anderson Cancer Center, Houston, TX, USA
| | - Alexander Biederstädt
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas, MD Anderson Cancer Center, Houston, TX, USA
- Department of Medicine III: Hematology and Oncology, School of Medicine, Technical University of Munich, Munich, Germany
| | - Katayoun Rezvani
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas, MD Anderson Cancer Center, Houston, TX, USA.
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27
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Tso HH, Galindo-González L, Locke T, Strelkov SE. Protocol: rhPCR and SNaPshot assays to distinguish Plasmodiophora brassicae pathotype clusters. PLANT METHODS 2022; 18:91. [PMID: 35780127 PMCID: PMC9250251 DOI: 10.1186/s13007-022-00923-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 06/21/2022] [Indexed: 05/08/2023]
Abstract
BACKGROUND Clubroot of canola (Brassica napus), caused by the soilborne pathogen Plasmodiophora brassicae, has become a serious threat to canola production in Canada. The deployment of clubroot-resistant (CR) cultivars is the most commonly used management strategy; however, the widespread cultivation of CR canola has resulted in the emergence of new pathotypes of P. brassicae capable of overcoming resistance. Several host differential sets have been reported for pathotype identification, but such testing is time-consuming, labor-intensive, and based on phenotypic classifications. The development of rapid and objective methods that allow for efficient, cost-effective and convenient pathotyping would enable testing of a much larger number of samples in shorter times. The aim of this study was to develop two pathotyping assays, an RNase H2-dependent PCR (rhPCR) assay and a SNaPshot assay, which could quickly differentiate P. brassicae pathotypes. RESULTS Both assays clearly distinguished between pathotype clusters in a collection of 38 single-spore isolates of P. brassicae. Additional isolates pathotyped from clubbed roots and samples from blind testing also were correctly clustered. The rhPCR assay generated clearly differentiating electrophoretic bands without non-specific amplification. The SNaPshot assay was able to detect down to a 10% relative allelic proportion in a 10:90 template mixture with both single-spore isolates and field isolates when evaluated in a relative abundance test. CONCLUSIONS This study describes the development of two rapid and sensitive technologies for P. brassicae pathotyping. The high-throughput potential and accuracy of both assays makes them promising as SNP-based pathotype identification tools for clubroot diagnostics. rhPCR is a highly sensitive approach that can be optimized into a quantitative assay, while the main advantages of SNaPshot are its ability to multiplex samples and alleles in a single reaction and the detection of up to four allelic variants per target site.
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Affiliation(s)
- Heather H Tso
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada
| | - Leonardo Galindo-González
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada
- Present Address: Ottawa Plant Laboratory, Science Branch, Canadian Food Inspection Agency, 3851 Fallowfield Road, Ottawa, ON, K2H 8P9, Canada
| | - Troy Locke
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
| | - Stephen E Strelkov
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada.
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28
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Kath J, Du W, Pruene A, Braun T, Thommandru B, Turk R, Sturgeon ML, Kurgan GL, Amini L, Stein M, Zittel T, Martini S, Ostendorf L, Wilhelm A, Akyüz L, Rehm A, Höpken UE, Pruß A, Künkele A, Jacobi AM, Volk HD, Schmueck-Henneresse M, Stripecke R, Reinke P, Wagner DL. Pharmacological interventions enhance virus-free generation of TRAC-replaced CAR T cells. Mol Ther Methods Clin Dev 2022; 25:311-330. [PMID: 35573047 PMCID: PMC9062427 DOI: 10.1016/j.omtm.2022.03.018] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 03/29/2022] [Indexed: 12/30/2022]
Abstract
Chimeric antigen receptor (CAR) redirected T cells are potent therapeutic options against hematological malignancies. The current dominant manufacturing approach for CAR T cells depends on retroviral transduction. With the advent of gene editing, insertion of a CD19-CAR into the T cell receptor (TCR) alpha constant (TRAC) locus using adeno-associated viruses for gene transfer was demonstrated, and these CD19-CAR T cells showed improved functionality over their retrovirally transduced counterparts. However, clinical-grade production of viruses is complex and associated with extensive costs. Here, we optimized a virus-free genome-editing method for efficient CAR insertion into the TRAC locus of primary human T cells via nuclease-assisted homology-directed repair (HDR) using CRISPR-Cas and double-stranded template DNA (dsDNA). We evaluated DNA-sensor inhibition and HDR enhancement as two pharmacological interventions to improve cell viability and relative CAR knockin rates, respectively. While the toxicity of transfected dsDNA was not fully prevented, the combination of both interventions significantly increased CAR knockin rates and CAR T cell yield. Resulting TRAC-replaced CD19-CAR T cells showed antigen-specific cytotoxicity and cytokine production in vitro and slowed leukemia progression in a xenograft mouse model. Amplicon sequencing did not reveal significant indel formation at potential off-target sites with or without exposure to DNA-repair-modulating small molecules. With TRAC-integrated CAR+ T cell frequencies exceeding 50%, this study opens new perspectives to exploit pharmacological interventions to improve non-viral gene editing in T cells.
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Affiliation(s)
- Jonas Kath
- BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health (BIH) at Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
- Berlin Center for Advanced Therapies (BeCAT), Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Augustenburger Platz 1, 13353 Berlin, Germany
| | - Weijie Du
- BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health (BIH) at Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
- Berlin Center for Advanced Therapies (BeCAT), Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Augustenburger Platz 1, 13353 Berlin, Germany
| | - Alina Pruene
- Regenerative Immune Therapies Applied, Clinics of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
- German Center for Infection Research (DZIF), Hannover-Braunschweig Region, Germany
| | - Tobias Braun
- Regenerative Immune Therapies Applied, Clinics of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
- German Center for Infection Research (DZIF), Hannover-Braunschweig Region, Germany
| | | | - Rolf Turk
- Integrated DNA Technologies, Inc., Coralville, IA 52241, USA
| | | | - Gavin L. Kurgan
- Integrated DNA Technologies, Inc., Coralville, IA 52241, USA
| | - Leila Amini
- BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health (BIH) at Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
- Berlin Center for Advanced Therapies (BeCAT), Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Augustenburger Platz 1, 13353 Berlin, Germany
| | - Maik Stein
- Berlin Center for Advanced Therapies (BeCAT), Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Augustenburger Platz 1, 13353 Berlin, Germany
| | - Tatiana Zittel
- Berlin Center for Advanced Therapies (BeCAT), Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Augustenburger Platz 1, 13353 Berlin, Germany
| | - Stefania Martini
- BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health (BIH) at Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Lennard Ostendorf
- Department of Nephrology and Intensive Care Medicine, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Berlin, Germany
- Deutsches Rheuma-Forschungszentrum (DRFZ), A Leibniz Institute, Berlin, Germany
| | | | | | - Armin Rehm
- Department of Translational Tumorimmunology, Max-Delbrück-Center for Molecular Medicine (MDC), 13125 Berlin, Germany
| | - Uta E. Höpken
- Department of Microenvironmental Regulation in Autoimmunity and Cancer, Max-Delbrück-Center for Molecular Medicine (MDC), 13125 Berlin, Germany
| | - Axel Pruß
- Institute of Transfusion Medicine, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Berlin, Germany
| | - Annette Künkele
- Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Berlin, Germany
- Berlin Institute of Health (BIH) at Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
- German Cancer Consortium (DKTK), 10117 Berlin, Germany
| | | | - Hans-Dieter Volk
- BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health (BIH) at Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
- Berlin Center for Advanced Therapies (BeCAT), Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Augustenburger Platz 1, 13353 Berlin, Germany
- Institute of Medical Immunology, Campus Virchow-Klinikum, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Augustenburger Platz 1, 13353 Berlin, Germany
| | - Michael Schmueck-Henneresse
- BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health (BIH) at Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
- Berlin Center for Advanced Therapies (BeCAT), Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Augustenburger Platz 1, 13353 Berlin, Germany
| | - Renata Stripecke
- Regenerative Immune Therapies Applied, Clinics of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
- German Center for Infection Research (DZIF), Hannover-Braunschweig Region, Germany
- Clinic I for Internal Medicine, Cancer Center Cologne Essen, University Hospital Cologne, Cologne, Germany
| | - Petra Reinke
- BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health (BIH) at Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
- Berlin Center for Advanced Therapies (BeCAT), Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Augustenburger Platz 1, 13353 Berlin, Germany
| | - Dimitrios L. Wagner
- BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health (BIH) at Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
- Berlin Center for Advanced Therapies (BeCAT), Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Augustenburger Platz 1, 13353 Berlin, Germany
- Institute of Transfusion Medicine, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Berlin, Germany
- Institute of Medical Immunology, Campus Virchow-Klinikum, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Augustenburger Platz 1, 13353 Berlin, Germany
- Corresponding author Dimitrios Laurin Wagner, MD, PhD, Berlin Center for Advanced Therapies (BeCAT) BIH Center for Regenerative Therapies (BCRT) Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Augustenburger Platz 1, 13353 Berlin, Germany.
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29
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Assessment of the Real-Time PCR Method Claiming to be Specific for Detection and Quantification of the First Commercialised Genome-Edited Plant. FOOD ANAL METHOD 2022. [DOI: 10.1007/s12161-022-02237-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Abstract
A real-time PCR method was recently published with a claim to be specific for the detection and identification of some genome-edited oilseed rape (OSR) lines commercialised in North America. The method was designed to detect a single base mutation in the AHAS1C gene, which confers herbicide tolerance. The authors claim that the method is event-specific for the genome-edited OSR line 5715 and fulfils all requirements for GMO analytical methods according to EU regulations. We have thoroughly assessed the method in relation to the minimum performance requirements (MPR) established by the European Network of GMO Laboratories (ENGL). The method was found to be sufficiently sensitive and robust when tested with pure genomic DNA of the OSR line 40 K. However, our results show that the method is not event-specific and detects also OSR lines carrying the same point mutation caused by somaclonal variation. Moreover, impaired robustness was observed using non-modified genomic DNA at the amount specified in the original protocol. Significant non-specific PCR amplifications with PCR products as non-target template DNA and with genomic DNA from numerous OSR varieties as well as from wild radish were found by three ISO/IEC 17025 accredited reference laboratories in tests using different master mixes and PCR cycler models. The assessment shows that the method does not meet the MPR for qualitative PCR methods and therefore is not fit-for-purpose for official controls of genetically modified products in the EU. Suggestions are provided for conditions under which analytical methods for genome-edited organisms should be validated.
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30
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Poh SE, Koh WL, Lim SYD, Wang EC, Yew YW, Common JE, Oon HH, Li H. Expression of Staphylococcus aureus virulence factors in atopic dermatitis. JID INNOVATIONS 2022; 2:100130. [PMID: 35860448 PMCID: PMC9289736 DOI: 10.1016/j.xjidi.2022.100130] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 03/23/2022] [Accepted: 03/28/2022] [Indexed: 11/29/2022] Open
Abstract
Atopic dermatitis (AD) is a skin inflammatory disease in which the opportunistic pathogen Staphylococcus aureus is prevalent and abundant. S. aureus harbors several secreted virulence factors that have well-studied functions in infection models, but it is unclear whether these extracellular microbial factors are relevant in the context of AD. To address this question, we designed a culture-independent method to detect and quantify S. aureus virulence factors expressed at the skin sites. We utilized RNase-H‒dependent multiplex PCR for preamplification of reverse-transcribed RNA extracted from tape strips of patients with AD sampled at skin sites with differing severity and assessed the expression of a panel of S. aureus virulence factors using qPCR. We observed an increase in viable S. aureus abundance on sites with increased severity of disease, and many virulence factors were expressed at the AD skin sites. Surprisingly, we did not observe any significant upregulation of the virulence factors at the lesional sites compared with those at the nonlesional control. Overall, we utilized a robust assay to directly detect and quantify viable S. aureus and its associated virulence factors at the site of AD skin lesions. This method can be extended to study the expression of skin microbial genes at the sites of various dermatological conditions.
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Affiliation(s)
- Si En Poh
- Molecular Engineering Lab, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research, Singapore, Singapore
| | - Winston L.C. Koh
- Molecular Engineering Lab, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research, Singapore, Singapore
| | - Shi Yu Derek Lim
- National Skin Centre, National Healthcare Group, Singapore, Singapore
| | - Etienne C.E. Wang
- National Skin Centre, National Healthcare Group, Singapore, Singapore
- Skin Research Institute of Singapore, Singapore
| | - Yik Weng Yew
- National Skin Centre, National Healthcare Group, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - John E.A. Common
- ASTAR Skin Research Labs (ASRL), Agency for Science, Technology and Research, Singapore, Singapore
| | - Hazel H. Oon
- National Skin Centre, National Healthcare Group, Singapore, Singapore
| | - Hao Li
- Molecular Engineering Lab, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research, Singapore, Singapore
- Department of Chemistry, Faculty of Science, National University of Singapore, Singapore, Singapore
- Correspondence: Hao Li, Department of Chemistry, Faculty of Science, National University of Singapore, 4 Science Drive 2, S9 Level 12, Singapore 117544, Singapore.
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31
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Buck K, Worthington M. Genetic Diversity of Wild and Cultivated Muscadine Grapes ( Vitis rotundifolia Michx.). FRONTIERS IN PLANT SCIENCE 2022; 13:852130. [PMID: 35419015 PMCID: PMC8996184 DOI: 10.3389/fpls.2022.852130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 03/01/2022] [Indexed: 06/14/2023]
Abstract
The muscadine (Vitis rotundifolia syn. Muscadinia rotundifolia) is an American grape species native to the southeastern United States that has been cultivated for centuries. Muscadines are one of three grape species in subgenus Muscadinia with a chromosome number of 2n = 40 (V. rotundifolia, Vitis munsoniana, and Vitis popenoei), making them genetically distinct from the European wine and table grape (Vitis vinifera) and other species in subgenus Euvitis. Crop improvement efforts have been continuous since the late 19th century, yet the germplasm that served as the foundation for early muscadine breeding efforts was sourced from a relatively small portion of their native range, mostly in the coastal plains of North Carolina. This study used the rhAmpSeq Vitis core panel haplotype markers to genotype 194 Muscadinia accessions from five cultivated populations and 15 wild populations collected across their native range. Wild populations from the western half of the native range were generally less genetically differentiated than hypothesized, but were genetically distinct from the material used in both past and present breeding efforts. One population collected from coastal North Carolina grouped closely with V. munsoniana accessions despite being well outside the reported range for that species. Principal coordinate and structure analyses revealed three main groups within the 194 accessions: one for cultivated material, one for wild V. rotundifolia, and one for V. munsoniana and V. popenoei. At K = 5, structure results showed that more recent muscadine cultivars are further differentiated from wild accessions and varieties. These analyses confirmed our hypothesis that muscadine cultivars are genetically differentiated from their wild counterparts. This study also showed that genetic diversity in V. rotundifolia is not equally distributed across its native range and that the limited number of genotypes used in crop improvement efforts has not fully utilized the genetic diversity within the species.
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32
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Allen D, Weiss LE, Saguy A, Rosenberg M, Iancu O, Matalon O, Lee C, Beider K, Nagler A, Shechtman Y, Hendel A. High-throughput Imaging of CRISPR- and Recombinant Adeno-associated Virus-induced DNA Damage Response in Human Hematopoietic Stem and Progenitor Cells. CRISPR J 2022; 5:80-94. [PMID: 35049367 PMCID: PMC8892977 DOI: 10.1089/crispr.2021.0128] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
CRISPR-Cas technology has revolutionized gene editing, but concerns remain due to its propensity for off-target interactions. This, combined with genotoxicity related to both CRISPR-Cas9-induced double-strand breaks and transgene delivery, poses a significant liability for clinical genome-editing applications. Current best practice is to optimize genome-editing parameters in preclinical studies. However, quantitative tools that measure off-target interactions and genotoxicity are costly and time-consuming, limiting the practicality of screening large numbers of potential genome-editing reagents and conditions. Here, we show that flow-based imaging facilitates DNA damage characterization of hundreds of human hematopoietic stem and progenitor cells per minute after treatment with CRISPR-Cas9 and recombinant adeno-associated virus serotype 6. With our web-based platform that leverages deep learning for image analysis, we find that greater DNA damage response is observed for guide RNAs with higher genome-editing activity, differentiating even single on-target guide RNAs with different levels of off-target interactions. This work simplifies the characterization and screening process of genome-editing parameters toward enabling safer and more effective gene-therapy applications.
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Affiliation(s)
- Daniel Allen
- Institute of Nanotechnology and Advanced Materials, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Lucien E Weiss
- Department of Biomedical Engineering, Technion, Haifa, Israel.,Department of Engineering Physics, Polytechnique Montreal, Canada
| | - Alon Saguy
- Department of Biomedical Engineering, Technion, Haifa, Israel
| | - Michael Rosenberg
- Institute of Nanotechnology and Advanced Materials, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Ortal Iancu
- Institute of Nanotechnology and Advanced Materials, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Omri Matalon
- Arazi School of Computer Science, Interdisciplinary Center, Herzliya, Israel
| | - Ciaran Lee
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Katia Beider
- Division of Hematology and Bone Marrow Transplantation, Chaim Sheba Medical Center, Tel-Hashomer, Ramat Gan, Israel
| | - Arnon Nagler
- Division of Hematology and Bone Marrow Transplantation, Chaim Sheba Medical Center, Tel-Hashomer, Ramat Gan, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Yoav Shechtman
- Department of Biomedical Engineering, Technion, Haifa, Israel
| | - Ayal Hendel
- Institute of Nanotechnology and Advanced Materials, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
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Srivastava RK, Satyavathi CT, Mahendrakar MD, Singh RB, Kumar S, Govindaraj M, Ghazi IA. Addressing Iron and Zinc Micronutrient Malnutrition Through Nutrigenomics in Pearl Millet: Advances and Prospects. Front Genet 2021; 12:723472. [PMID: 34868202 PMCID: PMC8637740 DOI: 10.3389/fgene.2021.723472] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 09/23/2021] [Indexed: 11/23/2022] Open
Abstract
Iron (Fe) and zinc (Zn) micronutrient deficiencies are significant health concerns, particularly among the underprivileged and resource-poor people in the semi-arid tropics globally. Pearl millet is regarded as a climate-smart crop with low water and energy footprints. It thrives well under adverse agro-ecologies such as high temperatures and limited rainfall. Pearl millet is regarded as a nutri-cereal owing to health-promoting traits such as high grain Fe and Zn content, metabolizable energy, high antioxidant and polyphenols, high proportion of slowly digestible starches, dietary fibers, and favorable essential amino acid profile compared to many cereals. Higher genetic variability for grain Fe and Zn content has facilitated considerable progress in mapping and mining QTLs, alleles and genes underlying micronutrient metabolism. This has been made possible by developing efficient genetic and genomic resources in pearl millet over the last decade. These include genetic stocks such as bi-parental RIL mapping populations, association mapping panels, chromosome segment substitution lines (CSSLs) and TILLING populations. On the genomics side, considerable progress has been made in generating genomic markers, such as SSR marker repository development. This was followed by the development of a next-generation sequencing-based genome-wide SNP repository. The circa 1,000 genomes re-sequencing project played a significant role. A high-quality reference genome was made available by re-sequencing of world diversity panel, mapping population parents and hybrid parental lines. This mini-review attempts to provide information on the current developments on mapping Fe and Zn content in pearl millet and future outlook.
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Affiliation(s)
- Rakesh K Srivastava
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - C Tara Satyavathi
- All India Coordinated Research Project on Pearl Millet (Indian Council of Agricultural Research), Jodhpur, India
| | - Mahesh D Mahendrakar
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Ram B Singh
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Sushil Kumar
- Department of Agricultural Biotechnology, Anand Agricultural University (AAU), Anand, India
| | - Mahalingam Govindaraj
- Alliance of Bioversity International and the International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - Irfan A Ghazi
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, India
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Biederstädt A, Rezvani K. Engineering the next generation of CAR-NK immunotherapies. Int J Hematol 2021; 114:554-571. [PMID: 34453686 PMCID: PMC8397867 DOI: 10.1007/s12185-021-03209-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 08/13/2021] [Accepted: 08/18/2021] [Indexed: 12/12/2022]
Abstract
Over the past few years, cellular immunotherapy has emerged as a novel treatment option for certain forms of hematologic malignancies with multiple CAR-T therapies now routinely administered in the clinic. The limitations of generating an autologous cell product and the challenges of toxicity with CAR-T cells underscore the need to develop novel cell therapy products that are universal, safe, and potent. Natural killer (NK) cells are part of the innate immune system with unique advantages, including the potential for off-the-shelf therapy. A recent first-in-human trial of CD19-CAR-NK infusion in patients with relapsed/refractory lymphoid malignancies proved safe with promising clinical activity. Building on these encouraging clinical responses, research is now actively exploring ways to further enhance CAR-NK cell potency by prolonging in vivo persistence and overcoming mechanisms of functional exhaustion. Besides these strategies to modulate CAR-NK cell intrinsic properties, there are increasing efforts to translate the successes seen in hematologic malignancies to the solid tumor space. This review will provide an overview on current trends and evolving concepts to genetically engineer the next generation of CAR-NK therapies. Emphasis will be placed on innovative multiplexed engineering approaches including CRISPR/Cas9 to overcome CAR-NK functional exhaustion and reprogram immune cell metabolism for enhanced potency.
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Affiliation(s)
- Alexander Biederstädt
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Unit 423, Houston, TX, USA
- Department of Medicine III, Hematology/Oncology, Klinikum rechts der Isar, Technical University of Munich, Ismaninger Str. 22, 81675, Munich, Germany
| | - Katayoun Rezvani
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Unit 423, Houston, TX, USA.
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35
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van Essen M, Riepsaame J, Jacob J. CRISPR-Cas Gene Perturbation and Editing in Human Induced Pluripotent Stem Cells. CRISPR J 2021; 4:634-655. [PMID: 34582693 DOI: 10.1089/crispr.2021.0063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Directing the fates of human pluripotent stem cells (hPSC) to generate a multitude of differentiated cell types allows the study of the genetic regulation of human development and disease. The translational potential of hPSC is maximized by exploiting CRISPR to silence or activate genes with spatial and temporal precision permanently or reversibly. Here, we summarize the increasingly refined and diverse CRISPR toolkit for the latter forms of gene perturbation in hPSC and their downstream applications. We discuss newer methods to install edits efficiently with single nucleotide resolution and describe pooled CRISPR screens as a powerful means of unbiased discovery of genes associated with a phenotype of interest. Last, we discuss the potential of these combined technologies in the treatment of hitherto intractable human diseases and the challenges to their implementation in the clinic.
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Affiliation(s)
- Max van Essen
- Nuffield Department of Clinical Neurosciences, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom; and University of Oxford, Oxford, United Kingdom
| | - Joey Riepsaame
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - John Jacob
- Nuffield Department of Clinical Neurosciences, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom; and University of Oxford, Oxford, United Kingdom
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36
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Atkins A, Chung CH, Allen AG, Dampier W, Gurrola TE, Sariyer IK, Nonnemacher MR, Wigdahl B. Off-Target Analysis in Gene Editing and Applications for Clinical Translation of CRISPR/Cas9 in HIV-1 Therapy. Front Genome Ed 2021; 3:673022. [PMID: 34713260 PMCID: PMC8525399 DOI: 10.3389/fgeed.2021.673022] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 06/21/2021] [Indexed: 12/26/2022] Open
Abstract
As genome-editing nucleases move toward broader clinical applications, the need to define the limits of their specificity and efficiency increases. A variety of approaches for nuclease cleavage detection have been developed, allowing a full-genome survey of the targeting landscape and the detection of a variety of repair outcomes for nuclease-induced double-strand breaks. Each approach has advantages and disadvantages relating to the means of target-site capture, target enrichment mechanism, cellular environment, false discovery, and validation of bona fide off-target cleavage sites in cells. This review examines the strengths, limitations, and origins of the different classes of off-target cleavage detection systems including anchored primer enrichment (GUIDE-seq), in situ detection (BLISS), in vitro selection libraries (CIRCLE-seq), chromatin immunoprecipitation (ChIP) (DISCOVER-Seq), translocation sequencing (LAM PCR HTGTS), and in vitro genomic DNA digestion (Digenome-seq and SITE-Seq). Emphasis is placed on the specific modifications that give rise to the enhanced performance of contemporary techniques over their predecessors and the comparative performance of techniques for different applications. The clinical relevance of these techniques is discussed in the context of assessing the safety of novel CRISPR/Cas9 HIV-1 curative strategies. With the recent success of HIV-1 and SIV-1 viral suppression in humanized mice and non-human primates, respectively, using CRISPR/Cas9, rigorous exploration of potential off-target effects is of critical importance. Such analyses would benefit from the application of the techniques discussed in this review.
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Affiliation(s)
- Andrew Atkins
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United States,Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Cheng-Han Chung
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United States,Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Alexander G. Allen
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United States,Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Will Dampier
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United States,Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Theodore E. Gurrola
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United States,Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Ilker K. Sariyer
- Department of Neuroscience and Center for Neurovirology, Temple University Lewis Katz School of Medicine, Philadelphia, PA, United States
| | - Michael R. Nonnemacher
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United States,Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Brian Wigdahl
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United States,Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States,Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, United States,*Correspondence: Brian Wigdahl
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Hasegawa T, Hapsari D, Iwahashi H. RNase H-dependent amplification improves the accuracy of rolling circle amplification combined with loop-mediated isothermal amplification (RCA-LAMP). PeerJ 2021; 9:e11851. [PMID: 34395086 PMCID: PMC8327969 DOI: 10.7717/peerj.11851] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 07/03/2021] [Indexed: 11/20/2022] Open
Abstract
The hybrid method upon combining rolling circle amplification and loop-mediated isothermal amplification (RCA-LAMP) was developed to quantify very small amount of different type of RNAs, such as miRNAs. RCA-LAMP can help detect short sequences through padlock probe (PLP) circularization and exhibit powerful DNA amplification. However, one of the factors that determines the detection limit of RCA-LAMP is non-specific amplification. In this study, we improved the accuracy of RCA-LAMP through applying RNase H-dependent PCR (rhPCR) technology. In this method, the non-specific amplification was suppressed by using the rh primer, which is designed through blocking the modification at the 3'end to stop DNA polymerase reaction and replacing the 6th DNA molecule from the end with RNA using RNase H2 enzyme. Traditional RCA-LAMP amplified the non-specific amplicons from linear PLP without a targeting reaction, while RCA-LAMP with rh primer and RNase H2 suppressed the non-specific amplification. Conversely, we identified the risk posed upon conducting PLP cyclization reaction using Splint R ligase in the RNA-targeting step that occurred even in the RNA-negative condition, which is another factor determining the detection limit of RCA-LAMP. Therefore, this study contributes in improving the accuracy of RNA quantification using RCA-LAMP.
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Affiliation(s)
- Takema Hasegawa
- The United Graduate School of Agricultural Science, Gifu University, Gifu, Gifu, Japan.,Current affiliation: Research Institute for Material and Chemical Measurement, National Metrology Institute of Japan (NMIJ), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| | - Diana Hapsari
- The United Graduate School of Agricultural Science, Gifu University, Gifu, Gifu, Japan
| | - Hitoshi Iwahashi
- Faculty of Applied Biological Sciences, Gifu University, Gifu, Gifu, Japan
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38
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Current and Future Pathotyping Platforms for Plasmodiophora brassicae in Canada. PLANTS 2021; 10:plants10071446. [PMID: 34371649 PMCID: PMC8309272 DOI: 10.3390/plants10071446] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/06/2021] [Accepted: 07/12/2021] [Indexed: 11/17/2022]
Abstract
Clubroot, caused by Plasmodiophora brassicae, is one of the most detrimental threats to crucifers worldwide and has emerged as an important disease of canola (Brassica napus) in Canada. At present, pathotypes are distinguished phenotypically by their virulence patterns on host differential sets, including the systems of Williams, Somé et al., the European Clubroot Differential set, and most recently the Canadian Clubroot Differential set and the Sinitic Clubroot Differential set. Although these are frequently used because of their simplicity of application, they are time-consuming, labor-intensive, and can lack sensitivity. Early, preventative pathotype detection is imperative to maximize productivity and promote sustainable crop production. The decreased turnaround time and increased sensitivity and specificity of genotypic pathotyping will be valuable for the development of integrated clubroot management plans, and interest in molecular techniques to complement phenotypic methods is increasing. This review provides a synopsis of current and future molecular pathotyping platforms for P. brassicae and aims to provide information on techniques that may be most suitable for the development of rapid, reliable, and cost-effective pathotyping assays.
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Cristall K, Bidard FC, Pierga JY, Rauh MJ, Popova T, Sebbag C, Lantz O, Stern MH, Mueller CR. A DNA methylation-based liquid biopsy for triple-negative breast cancer. NPJ Precis Oncol 2021; 5:53. [PMID: 34135468 PMCID: PMC8209161 DOI: 10.1038/s41698-021-00198-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 06/02/2021] [Indexed: 12/12/2022] Open
Abstract
Here, we present a next-generation sequencing (NGS) methylation-based blood test called methylation DETEction of Circulating Tumour DNA (mDETECT) designed for the optimal detection and monitoring of metastatic triple-negative breast cancer (TNBC). Based on a highly multiplexed targeted sequencing approach, this assay incorporates features that offer superior performance and included 53 amplicons from 47 regions. Analysis of a previously characterised cohort of women with metastatic TNBC with limited quantities of plasma (<2 ml) produced an AUC of 0.92 for detection of a tumour with a sensitivity of 76% for a specificity of 100%. mDETECTTNBC was quantitative and showed superior performance to an NGS TP53 mutation-based test carried out on the same patients and to the conventional CA15-3 biomarker. mDETECT also functioned well in serum samples from metastatic TNBC patients where it produced an AUC of 0.97 for detection of a tumour with a sensitivity of 93% for a specificity of 100%. An assay for BRCA1 promoter methylation was also incorporated into the mDETECT assay and functioned well but its clinical significance is currently unclear. Clonal Hematopoiesis of Indeterminate Potential was investigated as a source of background in control subjects but was not seen to be significant, though a link to adiposity may be relevant. The mDETECTTNBC assay is a liquid biopsy able to quantitatively detect all TNBC cancers and has the potential to improve the management of patients with this disease.
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Affiliation(s)
- Katrina Cristall
- Queen's Cancer Research Institute, Queen's University, Kingston, ON, Canada.,Department of Pathology and Molecular Medicine, Queen's University, Kingston, ON, Canada
| | - Francois-Clement Bidard
- Circulating Tumor Biomarkers Laboratory, SiRIC, Translational Research Department, Institut Curie, Paris, France.,Department of Medical Oncology, Institut Curie, Paris, France
| | - Jean-Yves Pierga
- Circulating Tumor Biomarkers Laboratory, SiRIC, Translational Research Department, Institut Curie, Paris, France.,Department of Medical Oncology, Institut Curie, Paris, France.,Université Paris Descartes, Paris, France
| | - Michael J Rauh
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, ON, Canada
| | - Tatiana Popova
- INSERM U830 Cancer, Heterogeneity, Instability and Plasticity (CHIP), Institut Curie, Paris, France
| | - Clara Sebbag
- Department of Medical Oncology, Institut Curie, Paris, France
| | - Olivier Lantz
- Circulating Tumor Biomarkers Laboratory, SiRIC, Translational Research Department, Institut Curie, Paris, France.,INSERM CIC BT 1428, Institut Curie, Paris, France.,INSERM U932, Institut Curie, Paris, France
| | - Marc-Henri Stern
- INSERM U830 Cancer, Heterogeneity, Instability and Plasticity (CHIP), Institut Curie, Paris, France
| | - Christopher R Mueller
- Queen's Cancer Research Institute, Queen's University, Kingston, ON, Canada. .,Department of Pathology and Molecular Medicine, Queen's University, Kingston, ON, Canada. .,Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, Canada.
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40
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Higgins O, Smith TJ. 3' Tth Endonuclease Cleavage Polymerase Chain Reaction (3TEC-PCR) Technology for Single-Base-Specific Multiplex Pathogen Detection using a Two-Oligonucleotide System. Int J Mol Sci 2021; 22:6061. [PMID: 34199760 PMCID: PMC8199996 DOI: 10.3390/ijms22116061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 05/28/2021] [Accepted: 06/01/2021] [Indexed: 11/21/2022] Open
Abstract
Polymerase chain reaction (PCR) is the standard in nucleic acid amplification technology for infectious disease pathogen detection and has been the primary diagnostic tool employed during the global COVID-19 pandemic. Various PCR technology adaptations, typically using two-oligonucleotide dye-binding methods or three-oligonucleotide hydrolysis probe systems, enable real-time multiplex target detection or single-base specificity for the identification of single-nucleotide polymorphisms (SNPs). A small number of two-oligonucleotide PCR systems facilitating both multiplex detection and SNP identification have been reported; however, these methods often have limitations in terms of target specificity, production of variable or false-positive results, and the requirement for extensive optimisation or post-amplification analysis. This study introduces 3' Tth endonuclease cleavage PCR (3TEC-PCR), a two-oligonucleotide PCR system incorporating a modified primer/probe and a thermostable cleavage enzyme, Tth endonuclease IV, for real-time multiplex detection and SNP identification. Complete analytical specificity, low limits of detection, single-base specificity, and simultaneous multiple target detection have been demonstrated in this study using 3TEC-PCR to identify bacterial meningitis associated pathogens. This is the first report of a two-oligonucleotide, real-time multiplex PCR technology with single-base specificity using Tth endonuclease IV.
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Affiliation(s)
- Owen Higgins
- Molecular Diagnostics Research Group, School of Natural Sciences, National University of Ireland, Galway, Ireland;
- Centre for One Health, Ryan Institute, National University of Ireland, Galway, Ireland
| | - Terry J. Smith
- Molecular Diagnostics Research Group, School of Natural Sciences, National University of Ireland, Galway, Ireland;
- Centre for One Health, Ryan Institute, National University of Ireland, Galway, Ireland
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41
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Azevedo BT, Vercesi Filho AE, Gutmanis G, Verissimo CJ, Katiki LM, Okino CH, Cristina de Sena Oliveira M, Giglioti R. New sensitive methods for fraud detection in buffalo dairy products. Int Dairy J 2021. [DOI: 10.1016/j.idairyj.2021.105013] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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42
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Amit I, Iancu O, Levy-Jurgenson A, Kurgan G, McNeill MS, Rettig GR, Allen D, Breier D, Ben Haim N, Wang Y, Anavy L, Hendel A, Yakhini Z. CRISPECTOR provides accurate estimation of genome editing translocation and off-target activity from comparative NGS data. Nat Commun 2021; 12:3042. [PMID: 34031394 PMCID: PMC8144550 DOI: 10.1038/s41467-021-22417-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 03/04/2021] [Indexed: 12/26/2022] Open
Abstract
Controlling off-target editing activity is one of the central challenges in making CRISPR technology accurate and applicable in medical practice. Current algorithms for analyzing off-target activity do not provide statistical quantification, are not sufficiently sensitive in separating signal from noise in experiments with low editing rates, and do not address the detection of translocations. Here we present CRISPECTOR, a software tool that supports the detection and quantification of on- and off-target genome-editing activity from NGS data using paired treatment/control CRISPR experiments. In particular, CRISPECTOR facilitates the statistical analysis of NGS data from multiplex-PCR comparative experiments to detect and quantify adverse translocation events. We validate the observed results and show independent evidence of the occurrence of translocations in human cell lines, after genome editing. Our methodology is based on a statistical model comparison approach leading to better false-negative rates in sites with weak yet significant off-target activity.
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Affiliation(s)
- Ido Amit
- Arazi School of Computer Science, Interdisciplinary Center, Herzliya, Israel
| | - Ortal Iancu
- The Institute for Advanced Materials and Nanotechnology, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Alona Levy-Jurgenson
- Department of Computer Science, Technion-Israel Institute of Technology, Haifa, Israel
| | - Gavin Kurgan
- Integrated DNA Technologies Inc., Coralville, IA, USA
| | | | | | - Daniel Allen
- The Institute for Advanced Materials and Nanotechnology, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Dor Breier
- The Institute for Advanced Materials and Nanotechnology, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Nimrod Ben Haim
- The Institute for Advanced Materials and Nanotechnology, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Yu Wang
- Integrated DNA Technologies Inc., Coralville, IA, USA
| | - Leon Anavy
- Arazi School of Computer Science, Interdisciplinary Center, Herzliya, Israel
| | - Ayal Hendel
- The Institute for Advanced Materials and Nanotechnology, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel.
| | - Zohar Yakhini
- Arazi School of Computer Science, Interdisciplinary Center, Herzliya, Israel.
- Department of Computer Science, Technion-Israel Institute of Technology, Haifa, Israel.
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Large-scale GMP-compliant CRISPR-Cas9-mediated deletion of the glucocorticoid receptor in multivirus-specific T cells. Blood Adv 2021; 4:3357-3367. [PMID: 32717029 DOI: 10.1182/bloodadvances.2020001977] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 06/19/2020] [Indexed: 01/02/2023] Open
Abstract
Virus-specific T cells have proven highly effective for the treatment of severe and drug-refractory infections after hematopoietic stem cell transplant (HSCT). However, the efficacy of these cells is hindered by the use of glucocorticoids, often given to patients for the management of complications such as graft-versus-host disease. To address this limitation, we have developed a novel strategy for the rapid generation of good manufacturing practice (GMP)-grade glucocorticoid-resistant multivirus-specific T cells (VSTs) using clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9) gene-editing technology. We have shown that deleting the nuclear receptor subfamily 3 group C member 1 (NR3C1; the gene encoding for the glucocorticoid receptor) renders VSTs resistant to the lymphocytotoxic effect of glucocorticoids. NR3C1-knockout (KO) VSTs kill their targets and proliferate successfully in the presence of high doses of dexamethasone both in vitro and in vivo. Moreover, we developed a protocol for the rapid generation of GMP-grade NR3C1 KO VSTs with high on-target activity and minimal off-target editing. These genetically engineered VSTs promise to be a novel approach for the treatment of patients with life-threatening viral infections post-HSCT on glucocorticoid therapy.
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Next-generation cell therapies: the emerging role of CAR-NK cells. Blood Adv 2021; 4:5868-5876. [PMID: 33232480 DOI: 10.1182/bloodadvances.2020002547] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 08/30/2020] [Indexed: 12/12/2022] Open
Abstract
T cells engineered with chimeric antigen receptors (CARs) have revolutionized the field of cell therapy and changed the paradigm of treatment for many patients with relapsed or refractory B-cell malignancies. Despite this progress, there are limitations to CAR-T cell therapy in both the autologous and allogeneic settings, including practical, logistical, and toxicity issues. Given these concerns, there is a rapidly growing interest in natural killer cells as alternative vehicles for CAR engineering, given their unique biological features and their established safety profile in the allogeneic setting. Other immune effector cells, such as invariant natural killer T cells, γδ T cells, and macrophages, are attracting interest as well and eventually may be added to the repertoire of engineered cell therapies against cancer. The pace of these developments will undoubtedly benefit from multiple innovative technologies, such as the CRISPR-Cas gene editing system, which offers great potential to enhance the natural ability of immune effector cells to eliminate refractory cancers.
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45
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Fennell T, Zhang D, Isik M, Wang T, Gotta G, Wilson CJ, Marco E. CALITAS: A CRISPR-Cas-aware ALigner for In silico off-TArget Search. CRISPR J 2021; 4:264-274. [PMID: 33876962 DOI: 10.1089/crispr.2020.0036] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
We describe CALITAS, a CRISPR-Cas-aware aligner and integrated off-target search algorithm. CALITAS uses a modified and CRISPR-tuned version of the Needleman-Wunsch algorithm. It supports an unlimited number of mismatches and gaps and allows protospacer adjacent motif (PAM) mismatches or PAMless searches. CALITAS also includes an exhaustive search routine to scan genomes and genome variants provided with a standard Variant Call Format file. By default, CALITAS returns a single best alignment for a given off-target site, which is a significant improvement compared to other off-target algorithms, and it enables off-targets to be referenced directly using alignment coordinates. We validate and compare CALITAS using a selected set of target sites, as well as experimentally derived specificity data sets. In summary, CALITAS is a new tool for precise and relevant alignments and identification of candidate off-target sites across a genome. We believe it is the state of the art for CRISPR-Cas specificity assessments.
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Affiliation(s)
- Tim Fennell
- Fulcrum Genomics, Phoenix, Arizona, USA, Cambridge, Massachusetts, USA
| | - Deric Zhang
- Editas Medicine, Cambridge, Massachusetts, USA
| | - Meltem Isik
- Editas Medicine, Cambridge, Massachusetts, USA
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Disruptors, a new class of oligonucleotide reagents, significantly improved PCR performance on templates containing stable intramolecular secondary structures. Anal Biochem 2021; 624:114169. [PMID: 33766577 DOI: 10.1016/j.ab.2021.114169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 03/09/2021] [Accepted: 03/10/2021] [Indexed: 11/21/2022]
Abstract
Intramolecular secondary structures within templates have been shown to lower PCR performance. Whereas many approaches have been developed to mitigate such impairment on PCR, their effects can vary greatly depending on template sequences. Here we present a novel, universally effective approach to improve PCR performance involving specifically designed oligonucleotides called disruptors. A disruptor contained three functional components, an anchor designed to initiate template binding, an effector to disrupt intramolecular secondary structure, and a 3' blocker to prevent its elongation by DNA polymerase. A functional mechanism for a disruptor to improve PCR efficiency was proposed where anchor first binds to template followed by effector-mediated strand displacement to unwind intramolecular secondary structure. Such a mechanism was consistent with the observation that anchor played a more critical role for disruptor function. As an example of potential disruptor applications, inverted terminal repeat sequences of recombinant adeno-associated virus vectors were successfully amplified in the presence of disruptors despite their well-known reputation as some of the most difficult templates for PCR amplification and Sanger sequencing due to their ultra-stable T-shaped hairpin structures. In stark contrast, both DMSO and betaine, two PCR additives routinely used to facilitate PCR amplification and Sanger sequencing of GC-rich templates, did not demonstrate any improving effect.
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Daher M, Basar R, Gokdemir E, Baran N, Uprety N, Nunez Cortes AK, Mendt M, Kerbauy LN, Banerjee PP, Shanley M, Imahashi N, Li L, Lim FLWI, Fathi M, Rezvan A, Mohanty V, Shen Y, Shaim H, Lu J, Ozcan G, Ensley E, Kaplan M, Nandivada V, Bdiwi M, Acharya S, Xi Y, Wan X, Mak D, Liu E, Jiang XR, Ang S, Muniz-Feliciano L, Li Y, Wang J, Kordasti S, Petrov N, Varadarajan N, Marin D, Brunetti L, Skinner RJ, Lyu S, Silva L, Turk R, Schubert MS, Rettig GR, McNeill MS, Kurgan G, Behlke MA, Li H, Fowlkes NW, Chen K, Konopleva M, Champlin RE, Shpall EJ, Rezvani K. Targeting a cytokine checkpoint enhances the fitness of armored cord blood CAR-NK cells. Blood 2021; 137:624-636. [PMID: 32902645 PMCID: PMC7869185 DOI: 10.1182/blood.2020007748] [Citation(s) in RCA: 145] [Impact Index Per Article: 48.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 08/29/2020] [Indexed: 12/22/2022] Open
Abstract
Immune checkpoint therapy has resulted in remarkable improvements in the outcome for certain cancers. To broaden the clinical impact of checkpoint targeting, we devised a strategy that couples targeting of the cytokine-inducible Src homology 2-containing (CIS) protein, a key negative regulator of interleukin 15 (IL-15) signaling, with fourth-generation "armored" chimeric antigen receptor (CAR) engineering of cord blood-derived natural killer (NK) cells. This combined strategy boosted NK cell effector function through enhancing the Akt/mTORC1 axis and c-MYC signaling, resulting in increased aerobic glycolysis. When tested in a lymphoma mouse model, this combined approach improved NK cell antitumor activity more than either alteration alone, eradicating lymphoma xenografts without signs of any measurable toxicity. We conclude that targeting a cytokine checkpoint further enhances the antitumor activity of IL-15-secreting armored CAR-NK cells by promoting their metabolic fitness and antitumor activity. This combined approach represents a promising milestone in the development of the next generation of NK cells for cancer immunotherapy.
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Affiliation(s)
- May Daher
- Department of Stem Cell Transplantation and Cellular Therapy and
| | - Rafet Basar
- Department of Stem Cell Transplantation and Cellular Therapy and
| | - Elif Gokdemir
- Department of Stem Cell Transplantation and Cellular Therapy and
| | - Natalia Baran
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Nadima Uprety
- Department of Stem Cell Transplantation and Cellular Therapy and
| | | | - Mayela Mendt
- Department of Stem Cell Transplantation and Cellular Therapy and
| | - Lucila Nassif Kerbauy
- Department of Stem Cell Transplantation and Cellular Therapy and
- Department of Stem Cell Transplantation and Cellular Therapy, Hospital Israelita Albert Einstein, Sao Paulo, Brazil
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Biosciences Institute, University of Sao Paulo, Sao Paulo, Brazil
| | | | - Mayra Shanley
- Department of Stem Cell Transplantation and Cellular Therapy and
| | | | - Li Li
- Department of Stem Cell Transplantation and Cellular Therapy and
| | | | - Mohsen Fathi
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX
| | - Ali Rezvan
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX
| | - Vakul Mohanty
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Yifei Shen
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Hila Shaim
- Department of Stem Cell Transplantation and Cellular Therapy and
| | - Junjun Lu
- Department of Stem Cell Transplantation and Cellular Therapy and
| | - Gonca Ozcan
- Department of Stem Cell Transplantation and Cellular Therapy and
| | - Emily Ensley
- Department of Stem Cell Transplantation and Cellular Therapy and
| | - Mecit Kaplan
- Department of Stem Cell Transplantation and Cellular Therapy and
| | | | - Mustafa Bdiwi
- Department of Stem Cell Transplantation and Cellular Therapy and
| | - Sunil Acharya
- Department of Stem Cell Transplantation and Cellular Therapy and
| | - Yuanxin Xi
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Xinhai Wan
- Department of Stem Cell Transplantation and Cellular Therapy and
| | - Duncan Mak
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Enli Liu
- Department of Stem Cell Transplantation and Cellular Therapy and
| | - Xin Ru Jiang
- Department of Stem Cell Transplantation and Cellular Therapy and
| | - Sonny Ang
- Department of Stem Cell Transplantation and Cellular Therapy and
| | | | - Ye Li
- Department of Stem Cell Transplantation and Cellular Therapy and
| | - Jing Wang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Shahram Kordasti
- System Cancer Immunology, Comprehensive Cancer Centre, King's College London, London, United Kingdom
| | - Nedyalko Petrov
- System Cancer Immunology, Comprehensive Cancer Centre, King's College London, London, United Kingdom
| | - Navin Varadarajan
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX
| | - David Marin
- Department of Stem Cell Transplantation and Cellular Therapy and
| | - Lorenzo Brunetti
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX
| | | | - Shangrong Lyu
- C.T. Bauer College of Business, University of Houston, Houston, TX
| | - Leiser Silva
- C.T. Bauer College of Business, University of Houston, Houston, TX
| | - Rolf Turk
- Integrated DNA Technologies, Coralville, IA
| | | | | | | | | | | | - Heng Li
- Dana-Farber/Harvard Cancer Center, Boston, MA; and
| | - Natalie W Fowlkes
- Veterinary Medicine and Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Ken Chen
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Marina Konopleva
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | - Katayoun Rezvani
- Department of Stem Cell Transplantation and Cellular Therapy and
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48
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Massa AN, Bressano M, Soave JH, Buteler MI, Seijo G, Sobolev VS, Orner VA, Oddino C, Soave SJ, Faustinelli PC, de Blas FJ, Lamb MC, Arias RS. Genotyping tools and resources to assess peanut germplasm: smut-resistant landraces as a case study. PeerJ 2021; 9:e10581. [PMID: 33575123 PMCID: PMC7849506 DOI: 10.7717/peerj.10581] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 11/24/2020] [Indexed: 11/20/2022] Open
Abstract
Peanut smut caused by Thecaphora frezii is a severe fungal disease currently endemic to Argentina and Brazil. The identification of smut resistant germplasm is crucial in view of the potential risk of a global spread. In a recent study, we reported new sources of smut resistance and demonstrated its introgression into elite peanut cultivars. Here, we revisited one of these sources (line I0322) to verify its presence in the U.S. peanut germplasm collection and to identify single nucleotide polymorphisms (SNPs) potentially associated with resistance. Five accessions of Arachis hypogaea subsp. fastigiata from the U.S. peanut collection, along with the resistant source and derived inbred lines were genotyped with a 48K SNP peanut array. A recently developed SNP genotyping platform called RNase H2 enzyme-based amplification (rhAmp) was further applied to validate selected SNPs in a larger number of individuals per accession. More than 14,000 SNPs and nine rhAmp assays confirmed the presence of a germplasm in the U.S. peanut collection that is 98.6% identical (P < 0.01, bootstrap t-test) to the resistant line I0322. We report this germplasm with accompanying genetic information, genotyping data, and diagnostic SNP markers.
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Affiliation(s)
- Alicia N Massa
- National Peanut Research Laboratory, USDA-ARS, Dawson, GA, USA
| | - Marina Bressano
- Facultad de Ciencias Agropecuarias, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Juan H Soave
- Criadero El Carmen, General Cabrera, Córdoba, Argentina
| | | | - Guillermo Seijo
- Instituto de Botánica del Nordeste (IBONE, CONICET-UNNE) and Facultad de Ciencias Exactas y Naturales y Agrimensura, Universidad Nacional del Nordeste, Corrientes, Argentina
| | | | - Valerie A Orner
- National Peanut Research Laboratory, USDA-ARS, Dawson, GA, USA
| | | | - Sara J Soave
- Criadero El Carmen, General Cabrera, Córdoba, Argentina
| | | | - Francisco J de Blas
- Instituto Multidisciplinario de Biología Vegetal-(IMBIV-CONICET-UNC), Córdoba, Argentina
| | - Marshall C Lamb
- National Peanut Research Laboratory, USDA-ARS, Dawson, GA, USA
| | - Renee S Arias
- National Peanut Research Laboratory, USDA-ARS, Dawson, GA, USA
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NanoString Technology for Human Papillomavirus Typing. Viruses 2021; 13:v13020188. [PMID: 33513748 PMCID: PMC7911781 DOI: 10.3390/v13020188] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 01/20/2021] [Accepted: 01/24/2021] [Indexed: 12/20/2022] Open
Abstract
High-throughput HPV typing assays with increased automation, faster turnaround and type-specific digital readout would facilitate studies monitoring the impact of HPV vaccination. We evaluated the NanoString nCounter® platform for detection and digital readout of 48 HPV types in a single reaction. NanoString (NS) used proprietary software to design CodeSets: type-specific probe pairs targeting 48 HPV types and the globin gene. We tested residual DNA extracts from epidemiologic specimens and defined samples (HPV plasmids at 10 to 104 copies/reaction) directly (No-PCR) as well as after L1 consensus PCR of 45 (PCR-45) or 15 cycles (PCR-15). Assay and interpretation followed NS recommendations. We evaluated analytic performance by comparing NanoString results for types included in prior assays: Roche Linear Array (LA) or HPV TypeSeq assay. No-PCR results on 40 samples showed good type-specific agreement with LA (k = 0.621) but sensitivity was 65% with lower limit of detection (LOD) at 104 plasmid copies. PCR-45 results showed almost perfect type-specific agreement with LA (k = 0.862), 82% sensitivity and LOD at 10 copies. PCR-15 results on 75 samples showed substantial type-specific agreement with LA (k = 0.796, 92% sensitivity) and TypeSeq (k = 0.777, 87% sensitivity), and LOD at 10 copies of plasmids. This proof-of-principle study demonstrates the efficacy of the NS platform with HPV CodeSet for type-specific detection using a low number of PCR cycles (PCR-15). Studies are in progress to evaluate assay reproducibility and analytic validation with a larger number of samples.
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50
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Zeng Y, Koo KM, Shen AG, Hu JM, Trau M. Nucleic Acid Hybridization-Based Noise Suppression for Ultraselective Multiplexed Amplification of Mutant Variants. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2006370. [PMID: 33325632 DOI: 10.1002/smll.202006370] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 11/11/2020] [Indexed: 06/12/2023]
Abstract
The analysis of mutant nucleic acid (NA) variants can provide crucial clinical and biological insights for many diseases. Yet, existing analysis techniques are generally constrained by nonspecific "noise" signals from excessive wildtype background sequences, especially under rapid isothermal multiplexed target amplification conditions. Herein, the molecular hybridization chemistry between NA bases is manipulated to suppress noise signals and achieve ultraselective multiplexed detection of cancer gene fusion NA variants. Firstly, modified locked NA (LNA) bases are rationally introduced into oligonucleotide sequences as designed "locker probes" for high affinity hybridization to wildtype sequences, leading to enrichment of mutant variants for multiplexed isothermal amplification. Secondly, locker probes are coupled with a customized "proximity-programmed" (SERS) readout which allows precise control of hybridization-based plasmonic signaling to specifically detect multiple target amplicons within a single reaction. Moreover, the use of triple bond Raman reporters endows NA noise signal-free quantification in the Raman silent region (≈1800-2600 cm-1 ). With this dual molecular hybridization-based strategy, ultraselective multiplexed detection of gene fusion NA variants in cancer cellular models is actualized with successful noise suppression of native wildtype sequences. The distinct benefits of isothermal NA amplification and SERS multiplexing ability are simultaneously harnessed.
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Affiliation(s)
- Yi Zeng
- School of Printing and Packaging, Wuhan University, Wuhan, 430079, P. R. China
- The Centre of Analysis and Measurement of Wuhan University, Wuhan University, Wuhan, 430072, P. R. China
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, P. R. China
- Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Kevin M Koo
- Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD, 4072, Australia
- XING Technologies Pty Ltd, Sinnamon Park, Brisbane, QLD, 4073, Australia
- The University of Queensland Centre for Clinical Research (UQCCR), Brisbane, QLD, 4029, Australia
| | - Ai-Guo Shen
- School of Printing and Packaging, Wuhan University, Wuhan, 430079, P. R. China
| | - Ji-Ming Hu
- The Centre of Analysis and Measurement of Wuhan University, Wuhan University, Wuhan, 430072, P. R. China
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, P. R. China
| | - Matt Trau
- Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD, 4072, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
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